Starting phenix.real_space_refine on Thu Jul 2 03:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wl9_66050/07_2026/9wl9_66050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wl9_66050/07_2026/9wl9_66050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wl9_66050/07_2026/9wl9_66050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wl9_66050/07_2026/9wl9_66050.map" model { file = "/net/cci-nas-00/data/ceres_data/9wl9_66050/07_2026/9wl9_66050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wl9_66050/07_2026/9wl9_66050.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 3846 2.51 5 N 1116 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6132 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Chain: "C" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Chain: "E" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Time building chain proxies: 1.59, per 1000 atoms: 0.26 Number of scatterers: 6132 At special positions: 0 Unit cell: (146.01, 146.01, 42.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1122 8.00 N 1116 7.00 C 3846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 23 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 124 " distance=2.02 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 124 " distance=2.02 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 42 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 23 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 124 " distance=2.02 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 23 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 124 " distance=2.02 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 42 " distance=2.03 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 23 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 124 " distance=2.02 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 42 " distance=2.03 Simple disulfide: pdb=" SG CYS F 18 " - pdb=" SG CYS F 23 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 124 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 249.3 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 6 removed outlier: 8.799A pdb=" N TRP A 3 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N ILE C 6 " --> pdb=" O TRP A 3 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN A 5 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 4 " --> pdb=" O TRP E 3 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN E 5 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 19 removed outlier: 6.139A pdb=" N SER A 12 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE C 15 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU A 14 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR C 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 16 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP C 19 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N CYS A 18 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP A 19 " --> pdb=" O CYS E 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.385A pdb=" N TYR A 26 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLN E 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA A 28 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 35 through 41 removed outlier: 7.140A pdb=" N HIS A 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL C 38 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY A 37 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 40 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU E 41 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 49 removed outlier: 6.594A pdb=" N VAL A 48 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 52 through 60 removed outlier: 6.906A pdb=" N THR A 53 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY C 54 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N MET A 55 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE C 56 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 59 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU C 60 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N PHE A 52 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 10.831A pdb=" N MET E 55 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N GLY A 54 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N VAL E 57 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE A 56 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN E 59 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY A 58 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.813A pdb=" N VAL C 73 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG A 74 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 73 " --> pdb=" O GLY E 72 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARG E 74 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.254A pdb=" N ARG A 78 " --> pdb=" O GLY C 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 83 through 87 removed outlier: 6.166A pdb=" N MET A 84 " --> pdb=" O PHE E 85 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ILE E 87 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR A 86 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 98 removed outlier: 6.103A pdb=" N ILE A 96 " --> pdb=" O LYS C 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.537A pdb=" N THR A 104 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 111 removed outlier: 5.944A pdb=" N LEU A 108 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL C 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LYS A 110 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 111 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.724A pdb=" N GLY A 114 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 119 through 123 removed outlier: 6.467A pdb=" N HIS A 120 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ASN E 123 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 122 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 6 removed outlier: 8.861A pdb=" N TRP B 3 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N ILE D 6 " --> pdb=" O TRP B 3 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN B 5 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA B 4 " --> pdb=" O TRP F 3 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN F 5 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 12 through 19 removed outlier: 6.200A pdb=" N SER B 12 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE D 15 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU B 14 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR D 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG B 16 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP D 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N CYS B 18 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP B 19 " --> pdb=" O CYS F 18 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 26 through 29 removed outlier: 6.374A pdb=" N TYR B 26 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLN F 29 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA B 28 " --> pdb=" O GLN F 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 35 through 41 removed outlier: 6.790A pdb=" N GLN B 36 " --> pdb=" O HIS D 35 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY D 37 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 38 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP D 39 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N HIS B 35 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL F 38 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N GLY B 37 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N VAL F 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.594A pdb=" N VAL B 48 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 52 through 60 removed outlier: 6.937A pdb=" N THR B 53 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY D 54 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET B 55 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 56 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN B 59 " --> pdb=" O GLY D 58 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU D 60 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N PHE B 52 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N MET F 55 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLY B 54 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N VAL F 57 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE B 56 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN F 59 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY B 58 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 66 through 75 removed outlier: 6.877A pdb=" N VAL D 73 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG B 74 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN B 67 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASN F 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE B 69 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLY F 72 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ASN B 71 " --> pdb=" O GLY F 72 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG F 74 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 73 " --> pdb=" O ARG F 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 78 through 79 removed outlier: 6.255A pdb=" N ARG B 78 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 83 through 87 removed outlier: 6.097A pdb=" N MET B 84 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE F 87 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR B 86 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.146A pdb=" N ILE B 96 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 104 through 105 removed outlier: 6.506A pdb=" N THR B 104 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 108 through 111 removed outlier: 6.005A pdb=" N LEU B 108 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL D 111 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LYS B 110 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 111 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 119 through 123 removed outlier: 6.321A pdb=" N VAL B 119 " --> pdb=" O HIS D 120 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU D 122 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 121 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 130 through 132 removed outlier: 6.589A pdb=" N THR B 130 " --> pdb=" O ALA D 131 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2028 1.34 - 1.46: 1335 1.46 - 1.58: 2853 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6276 Sorted by residual: bond pdb=" CA ALA F 44 " pdb=" C ALA F 44 " ideal model delta sigma weight residual 1.532 1.517 0.015 9.60e-03 1.09e+04 2.45e+00 bond pdb=" CA ALA D 44 " pdb=" C ALA D 44 " ideal model delta sigma weight residual 1.532 1.517 0.015 9.60e-03 1.09e+04 2.43e+00 bond pdb=" CA CYS A 81 " pdb=" C CYS A 81 " ideal model delta sigma weight residual 1.532 1.518 0.015 9.60e-03 1.09e+04 2.34e+00 bond pdb=" CA ALA B 44 " pdb=" C ALA B 44 " ideal model delta sigma weight residual 1.532 1.518 0.015 9.60e-03 1.09e+04 2.28e+00 bond pdb=" CA HIS A 21 " pdb=" C HIS A 21 " ideal model delta sigma weight residual 1.527 1.508 0.019 1.27e-02 6.20e+03 2.23e+00 ... (remaining 6271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 7597 1.13 - 2.27: 660 2.27 - 3.40: 140 3.40 - 4.54: 51 4.54 - 5.67: 24 Bond angle restraints: 8472 Sorted by residual: angle pdb=" N HIS D 118 " pdb=" CA HIS D 118 " pdb=" C HIS D 118 " ideal model delta sigma weight residual 110.91 115.55 -4.64 1.17e+00 7.31e-01 1.58e+01 angle pdb=" N HIS F 118 " pdb=" CA HIS F 118 " pdb=" C HIS F 118 " ideal model delta sigma weight residual 110.91 115.54 -4.63 1.17e+00 7.31e-01 1.57e+01 angle pdb=" N HIS B 118 " pdb=" CA HIS B 118 " pdb=" C HIS B 118 " ideal model delta sigma weight residual 110.91 115.51 -4.60 1.17e+00 7.31e-01 1.55e+01 angle pdb=" N HIS E 21 " pdb=" CA HIS E 21 " pdb=" C HIS E 21 " ideal model delta sigma weight residual 111.74 107.26 4.48 1.35e+00 5.49e-01 1.10e+01 angle pdb=" N HIS C 21 " pdb=" CA HIS C 21 " pdb=" C HIS C 21 " ideal model delta sigma weight residual 111.74 107.32 4.42 1.35e+00 5.49e-01 1.07e+01 ... (remaining 8467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3418 17.55 - 35.09: 278 35.09 - 52.64: 111 52.64 - 70.18: 27 70.18 - 87.73: 12 Dihedral angle restraints: 3846 sinusoidal: 1596 harmonic: 2250 Sorted by residual: dihedral pdb=" CA VAL F 119 " pdb=" C VAL F 119 " pdb=" N HIS F 120 " pdb=" CA HIS F 120 " ideal model delta harmonic sigma weight residual -180.00 -155.86 -24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL D 119 " pdb=" C VAL D 119 " pdb=" N HIS D 120 " pdb=" CA HIS D 120 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL B 119 " pdb=" C VAL B 119 " pdb=" N HIS B 120 " pdb=" CA HIS B 120 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 3843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 456 0.031 - 0.061: 228 0.061 - 0.092: 77 0.092 - 0.122: 76 0.122 - 0.153: 45 Chirality restraints: 882 Sorted by residual: chirality pdb=" CA ILE B 87 " pdb=" N ILE B 87 " pdb=" C ILE B 87 " pdb=" CB ILE B 87 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ILE F 87 " pdb=" N ILE F 87 " pdb=" C ILE F 87 " pdb=" CB ILE F 87 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE D 87 " pdb=" N ILE D 87 " pdb=" C ILE D 87 " pdb=" CB ILE D 87 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 879 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 85 " 0.013 2.00e-02 2.50e+03 1.42e-02 3.52e+00 pdb=" CG PHE B 85 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 85 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 85 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 85 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 85 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 85 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 85 " 0.014 2.00e-02 2.50e+03 1.41e-02 3.49e+00 pdb=" CG PHE F 85 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE F 85 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 85 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE F 85 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 85 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 85 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 85 " 0.014 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE D 85 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 85 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 85 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 85 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 85 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 85 " 0.000 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 918 2.78 - 3.31: 5542 3.31 - 3.84: 10732 3.84 - 4.37: 12247 4.37 - 4.90: 22146 Nonbonded interactions: 51585 Sorted by model distance: nonbonded pdb=" OXT LEU A 133 " pdb=" NZ LYS C 97 " model vdw 2.246 3.120 nonbonded pdb=" NZ LYS A 97 " pdb=" OXT LEU E 133 " model vdw 2.252 3.120 nonbonded pdb=" NZ LYS B 110 " pdb=" OD2 ASP F 125 " model vdw 2.257 3.120 nonbonded pdb=" OD2 ASP B 125 " pdb=" NZ LYS D 110 " model vdw 2.264 3.120 nonbonded pdb=" NH1 ARG A 20 " pdb=" OE2 GLU D 14 " model vdw 2.290 3.120 ... (remaining 51580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.410 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.004 0.032 6294 Z= 0.208 Angle : 0.799 5.671 8508 Z= 0.442 Chirality : 0.055 0.153 882 Planarity : 0.004 0.031 1116 Dihedral : 16.280 87.729 2376 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 33 TYR 0.021 0.003 TYR C 63 PHE 0.032 0.004 PHE B 85 TRP 0.005 0.002 TRP D 3 HIS 0.012 0.004 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 ( 6276) covalent geometry : angle 0.79423 / 0.44 ( 8472) SS BOND : bond 0.00451 / 0.28 ( 18) SS BOND : angle 1.56508 / 1.21 ( 36) hydrogen bonds : bond 0.19168 / 13.41 ( 86) hydrogen bonds : angle 8.98811 / 6.33 ( 258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.242 Fit side-chains REVERT: A 16 ARG cc_start: 0.7951 (mtt90) cc_final: 0.7618 (mtt90) REVERT: A 98 LYS cc_start: 0.6695 (mttt) cc_final: 0.5930 (tttp) REVERT: B 33 ARG cc_start: 0.8517 (mmm160) cc_final: 0.6465 (mmt90) REVERT: B 39 ASP cc_start: 0.8026 (t70) cc_final: 0.7764 (t0) REVERT: B 74 ARG cc_start: 0.7224 (mtt90) cc_final: 0.6392 (mtt180) REVERT: B 98 LYS cc_start: 0.7944 (mttt) cc_final: 0.7329 (ttpt) REVERT: B 122 GLU cc_start: 0.8167 (tt0) cc_final: 0.7856 (tp30) REVERT: C 16 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7775 (mtt90) REVERT: C 98 LYS cc_start: 0.6804 (mttt) cc_final: 0.6247 (tttp) REVERT: C 132 TYR cc_start: 0.8036 (p90) cc_final: 0.7527 (p90) REVERT: D 74 ARG cc_start: 0.7415 (mtt90) cc_final: 0.6498 (mtt180) REVERT: D 98 LYS cc_start: 0.8013 (mttt) cc_final: 0.7419 (ttpt) REVERT: E 98 LYS cc_start: 0.6929 (mttt) cc_final: 0.6215 (tttp) REVERT: F 33 ARG cc_start: 0.8388 (mmm160) cc_final: 0.6372 (mmt90) REVERT: F 39 ASP cc_start: 0.8015 (t70) cc_final: 0.7729 (t0) REVERT: F 74 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6425 (mtt180) REVERT: F 98 LYS cc_start: 0.7880 (mttt) cc_final: 0.7639 (mttm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1483 time to fit residues: 28.7550 Evaluate side-chains 126 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 67 ASN A 118 HIS A 123 ASN B 67 ASN ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 123 ASN D 67 ASN ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN F 67 ASN ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118668 restraints weight = 7889.746| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.45 r_work: 0.3405 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6294 Z= 0.213 Angle : 0.760 6.083 8508 Z= 0.395 Chirality : 0.054 0.148 882 Planarity : 0.004 0.039 1116 Dihedral : 7.895 87.865 876 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.75 % Allowed : 12.31 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.21), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 20 TYR 0.018 0.003 TYR F 132 PHE 0.022 0.002 PHE B 85 TRP 0.005 0.001 TRP F 3 HIS 0.013 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 ( 6276) covalent geometry : angle 0.75716 / 0.39 ( 8472) SS BOND : bond 0.00288 / 0.17 ( 18) SS BOND : angle 1.19514 / 0.91 ( 36) hydrogen bonds : bond 0.03163 / 2.22 ( 86) hydrogen bonds : angle 6.49496 / 4.51 ( 258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6668 (tt0) REVERT: A 59 GLN cc_start: 0.8619 (mp-120) cc_final: 0.8358 (mm110) REVERT: A 98 LYS cc_start: 0.6784 (mttt) cc_final: 0.5732 (tttp) REVERT: B 33 ARG cc_start: 0.8611 (mmm160) cc_final: 0.6931 (mpt180) REVERT: B 39 ASP cc_start: 0.8104 (t70) cc_final: 0.7858 (t0) REVERT: B 74 ARG cc_start: 0.6905 (mtt90) cc_final: 0.6065 (mtt180) REVERT: B 98 LYS cc_start: 0.8046 (mttt) cc_final: 0.7695 (mtmt) REVERT: B 110 LYS cc_start: 0.8703 (tttp) cc_final: 0.8125 (ttmm) REVERT: B 122 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: B 133 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7200 (tt) REVERT: C 16 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7798 (mtt90) REVERT: C 59 GLN cc_start: 0.8547 (mp10) cc_final: 0.8142 (mm-40) REVERT: C 74 ARG cc_start: 0.5877 (mtt90) cc_final: 0.5038 (ptt90) REVERT: C 98 LYS cc_start: 0.7181 (mttt) cc_final: 0.6177 (tttp) REVERT: C 112 TYR cc_start: 0.8245 (m-80) cc_final: 0.7860 (m-80) REVERT: C 122 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6497 (tt0) REVERT: C 132 TYR cc_start: 0.8000 (p90) cc_final: 0.7481 (p90) REVERT: D 39 ASP cc_start: 0.8280 (t70) cc_final: 0.8044 (t0) REVERT: D 74 ARG cc_start: 0.7485 (mtt90) cc_final: 0.6512 (mtt180) REVERT: D 98 LYS cc_start: 0.8039 (mttt) cc_final: 0.7471 (ttpt) REVERT: E 20 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7402 (mtm180) REVERT: E 98 LYS cc_start: 0.7107 (mttt) cc_final: 0.5978 (tttp) REVERT: E 102 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8277 (tt) REVERT: E 118 HIS cc_start: 0.7953 (m-70) cc_final: 0.7649 (m-70) REVERT: F 33 ARG cc_start: 0.8537 (mmm160) cc_final: 0.7060 (mpt180) REVERT: F 39 ASP cc_start: 0.7944 (t70) cc_final: 0.7694 (t0) REVERT: F 74 ARG cc_start: 0.7340 (mtt90) cc_final: 0.6609 (mtt180) REVERT: F 84 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7531 (tpp) REVERT: F 98 LYS cc_start: 0.7965 (mttt) cc_final: 0.7693 (mttm) outliers start: 25 outliers final: 12 residues processed: 148 average time/residue: 0.1242 time to fit residues: 21.8561 Evaluate side-chains 139 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 116 GLN ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114067 restraints weight = 7814.851| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.57 r_work: 0.3416 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6294 Z= 0.183 Angle : 0.716 5.921 8508 Z= 0.373 Chirality : 0.053 0.152 882 Planarity : 0.004 0.030 1116 Dihedral : 7.839 89.323 876 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.00 % Allowed : 14.11 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 20 TYR 0.017 0.002 TYR F 132 PHE 0.020 0.002 PHE D 85 TRP 0.003 0.001 TRP C 3 HIS 0.011 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 6276) covalent geometry : angle 0.71263 / 0.37 ( 8472) SS BOND : bond 0.00340 / 0.19 ( 18) SS BOND : angle 1.25539 / 0.94 ( 36) hydrogen bonds : bond 0.03113 / 2.16 ( 86) hydrogen bonds : angle 6.06714 / 4.25 ( 258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6818 (tt0) REVERT: A 98 LYS cc_start: 0.6806 (mttt) cc_final: 0.5659 (tttp) REVERT: B 33 ARG cc_start: 0.8703 (mmm160) cc_final: 0.6962 (mpt180) REVERT: B 39 ASP cc_start: 0.8202 (t70) cc_final: 0.7897 (t0) REVERT: B 67 ASN cc_start: 0.7760 (t0) cc_final: 0.7545 (t0) REVERT: B 74 ARG cc_start: 0.6845 (mtt90) cc_final: 0.6005 (mtt180) REVERT: B 98 LYS cc_start: 0.7788 (mttt) cc_final: 0.7476 (mtmt) REVERT: B 110 LYS cc_start: 0.8701 (tttp) cc_final: 0.8074 (ttmm) REVERT: B 122 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: B 133 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7112 (tt) REVERT: C 14 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6920 (tt0) REVERT: C 16 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7856 (mtt-85) REVERT: C 98 LYS cc_start: 0.7288 (mttt) cc_final: 0.6153 (tttp) REVERT: C 112 TYR cc_start: 0.8295 (m-80) cc_final: 0.7800 (m-80) REVERT: C 122 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: D 33 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8302 (mtp85) REVERT: D 39 ASP cc_start: 0.8312 (t70) cc_final: 0.8011 (t0) REVERT: D 74 ARG cc_start: 0.7400 (mtt90) cc_final: 0.6428 (mtt180) REVERT: D 98 LYS cc_start: 0.7980 (mttt) cc_final: 0.7422 (ttpt) REVERT: E 20 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7430 (mtm180) REVERT: E 98 LYS cc_start: 0.7172 (mttt) cc_final: 0.5960 (tttp) REVERT: E 118 HIS cc_start: 0.8017 (m-70) cc_final: 0.7754 (m-70) REVERT: F 33 ARG cc_start: 0.8616 (mmm160) cc_final: 0.6553 (mmt90) REVERT: F 39 ASP cc_start: 0.7967 (t70) cc_final: 0.7690 (t0) REVERT: F 74 ARG cc_start: 0.7366 (mtt90) cc_final: 0.6560 (mtt180) REVERT: F 84 MET cc_start: 0.7849 (tpp) cc_final: 0.7640 (tpp) REVERT: F 98 LYS cc_start: 0.8044 (mttt) cc_final: 0.7437 (ttpt) outliers start: 20 outliers final: 14 residues processed: 139 average time/residue: 0.1191 time to fit residues: 19.6292 Evaluate side-chains 141 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112053 restraints weight = 7876.914| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.58 r_work: 0.3396 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6294 Z= 0.240 Angle : 0.776 6.128 8508 Z= 0.404 Chirality : 0.055 0.154 882 Planarity : 0.004 0.039 1116 Dihedral : 7.994 88.671 876 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.90 % Allowed : 14.56 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.21), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 20 TYR 0.016 0.003 TYR A 92 PHE 0.021 0.003 PHE B 85 TRP 0.003 0.001 TRP E 3 HIS 0.012 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 ( 6276) covalent geometry : angle 0.77221 / 0.40 ( 8472) SS BOND : bond 0.00302 / 0.18 ( 18) SS BOND : angle 1.34880 / 1.00 ( 36) hydrogen bonds : bond 0.02969 / 2.02 ( 86) hydrogen bonds : angle 6.06202 / 4.25 ( 258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.235 Fit side-chains REVERT: A 14 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6843 (tt0) REVERT: A 16 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7541 (mtt-85) REVERT: A 98 LYS cc_start: 0.6915 (mttt) cc_final: 0.5699 (tttp) REVERT: B 33 ARG cc_start: 0.8768 (mmm160) cc_final: 0.6518 (mmt90) REVERT: B 39 ASP cc_start: 0.8210 (t70) cc_final: 0.7872 (t0) REVERT: B 67 ASN cc_start: 0.7824 (t0) cc_final: 0.7616 (t0) REVERT: B 74 ARG cc_start: 0.6908 (mtt90) cc_final: 0.5936 (mtt180) REVERT: B 98 LYS cc_start: 0.7795 (mttt) cc_final: 0.7487 (mtmt) REVERT: B 110 LYS cc_start: 0.8646 (tttp) cc_final: 0.8059 (ttmm) REVERT: B 122 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: B 133 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7110 (tt) REVERT: C 16 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7899 (mtt-85) REVERT: C 74 ARG cc_start: 0.6114 (mtt90) cc_final: 0.4947 (ptt90) REVERT: C 98 LYS cc_start: 0.7381 (mttt) cc_final: 0.6138 (tttp) REVERT: C 112 TYR cc_start: 0.8423 (m-80) cc_final: 0.7971 (m-80) REVERT: C 132 TYR cc_start: 0.8031 (p90) cc_final: 0.7516 (p90) REVERT: D 39 ASP cc_start: 0.8394 (t70) cc_final: 0.8082 (t0) REVERT: D 74 ARG cc_start: 0.7360 (mtt90) cc_final: 0.6382 (mtt180) REVERT: D 98 LYS cc_start: 0.7948 (mttt) cc_final: 0.7404 (ttpt) REVERT: E 20 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7453 (mtm180) REVERT: E 98 LYS cc_start: 0.7347 (mttt) cc_final: 0.6006 (tttp) REVERT: E 102 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8254 (tt) REVERT: E 118 HIS cc_start: 0.8045 (m-70) cc_final: 0.7781 (m-70) REVERT: F 14 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7276 (tp30) REVERT: F 33 ARG cc_start: 0.8701 (mmm160) cc_final: 0.6489 (mmt90) REVERT: F 39 ASP cc_start: 0.8077 (t70) cc_final: 0.7697 (t0) REVERT: F 74 ARG cc_start: 0.7417 (mtt90) cc_final: 0.6533 (mtt180) REVERT: F 98 LYS cc_start: 0.8044 (mttt) cc_final: 0.7400 (ttpt) outliers start: 26 outliers final: 18 residues processed: 146 average time/residue: 0.1309 time to fit residues: 22.6880 Evaluate side-chains 149 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 70 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN C 21 HIS F 36 GLN ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115801 restraints weight = 7934.479| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.54 r_work: 0.3401 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6294 Z= 0.134 Angle : 0.665 5.655 8508 Z= 0.349 Chirality : 0.052 0.148 882 Planarity : 0.004 0.035 1116 Dihedral : 7.722 89.381 876 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.55 % Allowed : 16.52 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 20 TYR 0.014 0.002 TYR D 86 PHE 0.019 0.002 PHE B 85 TRP 0.002 0.001 TRP F 3 HIS 0.009 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 6276) covalent geometry : angle 0.66290 / 0.35 ( 8472) SS BOND : bond 0.00301 / 0.18 ( 18) SS BOND : angle 1.03460 / 0.78 ( 36) hydrogen bonds : bond 0.02375 / 1.60 ( 86) hydrogen bonds : angle 5.77296 / 4.10 ( 258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6816 (tt0) REVERT: A 59 GLN cc_start: 0.8543 (mp-120) cc_final: 0.8258 (mm110) REVERT: A 98 LYS cc_start: 0.6958 (mttt) cc_final: 0.5824 (tttp) REVERT: B 33 ARG cc_start: 0.8635 (mmm160) cc_final: 0.6852 (mpt180) REVERT: B 39 ASP cc_start: 0.8196 (t70) cc_final: 0.7926 (t0) REVERT: B 74 ARG cc_start: 0.6854 (mtt90) cc_final: 0.6030 (mtt180) REVERT: B 98 LYS cc_start: 0.7876 (mttt) cc_final: 0.7512 (mtpt) REVERT: B 110 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8083 (ttmm) REVERT: B 122 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: B 133 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7154 (tt) REVERT: C 98 LYS cc_start: 0.7484 (mttt) cc_final: 0.6233 (tttp) REVERT: C 112 TYR cc_start: 0.8275 (m-80) cc_final: 0.7874 (m-80) REVERT: D 39 ASP cc_start: 0.8284 (t70) cc_final: 0.8021 (t0) REVERT: D 74 ARG cc_start: 0.7349 (mtt90) cc_final: 0.6401 (mtt180) REVERT: D 98 LYS cc_start: 0.7988 (mttt) cc_final: 0.7395 (ttpt) REVERT: E 20 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7621 (mtm180) REVERT: E 98 LYS cc_start: 0.7389 (mttt) cc_final: 0.7189 (mtmt) REVERT: E 118 HIS cc_start: 0.7977 (m-70) cc_final: 0.7756 (m-70) REVERT: F 14 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7364 (tp30) REVERT: F 33 ARG cc_start: 0.8568 (mmm160) cc_final: 0.6497 (mmt90) REVERT: F 74 ARG cc_start: 0.7415 (mtt90) cc_final: 0.6551 (mtt180) REVERT: F 98 LYS cc_start: 0.7983 (mttt) cc_final: 0.7419 (ttpt) outliers start: 17 outliers final: 11 residues processed: 141 average time/residue: 0.1313 time to fit residues: 21.9188 Evaluate side-chains 142 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS C 118 HIS ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112165 restraints weight = 7890.670| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.59 r_work: 0.3390 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6294 Z= 0.250 Angle : 0.779 6.357 8508 Z= 0.407 Chirality : 0.055 0.152 882 Planarity : 0.005 0.036 1116 Dihedral : 7.959 88.813 876 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.15 % Allowed : 17.27 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.21), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.017 0.003 TYR A 92 PHE 0.026 0.003 PHE B 85 TRP 0.003 0.001 TRP B 3 HIS 0.012 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 ( 6276) covalent geometry : angle 0.77557 / 0.41 ( 8472) SS BOND : bond 0.00346 / 0.22 ( 18) SS BOND : angle 1.37969 / 1.03 ( 36) hydrogen bonds : bond 0.02898 / 1.98 ( 86) hydrogen bonds : angle 6.04611 / 4.27 ( 258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.207 Fit side-chains REVERT: A 14 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6891 (tt0) REVERT: A 16 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7518 (mtt90) REVERT: A 59 GLN cc_start: 0.8504 (mp-120) cc_final: 0.8268 (mp-120) REVERT: A 98 LYS cc_start: 0.6922 (mttt) cc_final: 0.5744 (tttp) REVERT: B 33 ARG cc_start: 0.8726 (mmm160) cc_final: 0.6826 (mpt180) REVERT: B 39 ASP cc_start: 0.8214 (t70) cc_final: 0.7886 (t0) REVERT: B 74 ARG cc_start: 0.6912 (mtt90) cc_final: 0.5923 (mtt180) REVERT: B 98 LYS cc_start: 0.7833 (mttt) cc_final: 0.7490 (mtmt) REVERT: B 122 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: B 133 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7113 (tt) REVERT: C 98 LYS cc_start: 0.7482 (mttt) cc_final: 0.6178 (tttp) REVERT: C 112 TYR cc_start: 0.8407 (m-80) cc_final: 0.7976 (m-80) REVERT: C 132 TYR cc_start: 0.8033 (p90) cc_final: 0.7529 (p90) REVERT: D 74 ARG cc_start: 0.7363 (mtt90) cc_final: 0.6368 (mtt180) REVERT: D 98 LYS cc_start: 0.7991 (mttt) cc_final: 0.7377 (ttpt) REVERT: E 20 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7469 (mtm180) REVERT: E 98 LYS cc_start: 0.7435 (mttt) cc_final: 0.7197 (mtmt) REVERT: E 118 HIS cc_start: 0.8046 (m-70) cc_final: 0.7783 (m-70) REVERT: F 14 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7469 (tp30) REVERT: F 33 ARG cc_start: 0.8646 (mmm160) cc_final: 0.6448 (mmt90) REVERT: F 39 ASP cc_start: 0.8108 (t70) cc_final: 0.7720 (t0) REVERT: F 74 ARG cc_start: 0.7433 (mtt90) cc_final: 0.6524 (mtt180) REVERT: F 98 LYS cc_start: 0.7943 (mttt) cc_final: 0.7333 (ttpt) outliers start: 21 outliers final: 16 residues processed: 143 average time/residue: 0.1338 time to fit residues: 22.6094 Evaluate side-chains 143 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 18 optimal weight: 0.0980 chunk 28 optimal weight: 7.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119056 restraints weight = 7787.323| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.49 r_work: 0.3379 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6294 Z= 0.162 Angle : 0.699 5.789 8508 Z= 0.367 Chirality : 0.053 0.150 882 Planarity : 0.004 0.040 1116 Dihedral : 7.799 89.402 876 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.00 % Allowed : 17.42 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 16 TYR 0.014 0.002 TYR D 86 PHE 0.021 0.002 PHE B 85 TRP 0.002 0.001 TRP E 3 HIS 0.010 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 6276) covalent geometry : angle 0.69666 / 0.37 ( 8472) SS BOND : bond 0.00311 / 0.18 ( 18) SS BOND : angle 1.13005 / 0.85 ( 36) hydrogen bonds : bond 0.02472 / 1.68 ( 86) hydrogen bonds : angle 5.85773 / 4.17 ( 258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.249 Fit side-chains REVERT: A 14 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6842 (tt0) REVERT: A 16 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7493 (mtt90) REVERT: A 59 GLN cc_start: 0.8472 (mp-120) cc_final: 0.8209 (mp-120) REVERT: A 98 LYS cc_start: 0.6896 (mttt) cc_final: 0.5743 (tttp) REVERT: B 33 ARG cc_start: 0.8643 (mmm160) cc_final: 0.6786 (mpt180) REVERT: B 39 ASP cc_start: 0.8193 (t70) cc_final: 0.7845 (t0) REVERT: B 74 ARG cc_start: 0.6855 (mtt90) cc_final: 0.5886 (mtt180) REVERT: B 98 LYS cc_start: 0.7851 (mttt) cc_final: 0.7481 (mtmt) REVERT: B 122 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: B 133 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7128 (tt) REVERT: C 98 LYS cc_start: 0.7425 (mttt) cc_final: 0.6163 (tttp) REVERT: C 112 TYR cc_start: 0.8387 (m-80) cc_final: 0.7953 (m-80) REVERT: C 122 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6780 (tt0) REVERT: C 132 TYR cc_start: 0.8008 (p90) cc_final: 0.7493 (p90) REVERT: D 39 ASP cc_start: 0.8305 (t70) cc_final: 0.8028 (t0) REVERT: D 74 ARG cc_start: 0.7237 (mtt90) cc_final: 0.6272 (mtt180) REVERT: D 98 LYS cc_start: 0.8013 (mttt) cc_final: 0.7375 (ttpt) REVERT: E 20 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7616 (mtm180) REVERT: E 118 HIS cc_start: 0.8013 (m-70) cc_final: 0.7778 (m-70) REVERT: F 14 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7502 (tp30) REVERT: F 33 ARG cc_start: 0.8614 (mmm160) cc_final: 0.6404 (mmt90) REVERT: F 74 ARG cc_start: 0.7398 (mtt90) cc_final: 0.6506 (mtt180) REVERT: F 98 LYS cc_start: 0.7961 (mttt) cc_final: 0.7356 (ttpt) outliers start: 20 outliers final: 14 residues processed: 143 average time/residue: 0.1405 time to fit residues: 23.8183 Evaluate side-chains 144 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111926 restraints weight = 7976.912| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.59 r_work: 0.3389 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6294 Z= 0.259 Angle : 0.786 6.143 8508 Z= 0.411 Chirality : 0.055 0.156 882 Planarity : 0.005 0.040 1116 Dihedral : 7.962 87.806 876 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 3.45 % Allowed : 17.42 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 16 TYR 0.017 0.003 TYR A 92 PHE 0.028 0.003 PHE B 85 TRP 0.003 0.001 TRP E 3 HIS 0.014 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.26 ( 6276) covalent geometry : angle 0.78215 / 0.41 ( 8472) SS BOND : bond 0.00335 / 0.20 ( 18) SS BOND : angle 1.39254 / 1.05 ( 36) hydrogen bonds : bond 0.02949 / 1.99 ( 86) hydrogen bonds : angle 6.09069 / 4.30 ( 258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.243 Fit side-chains REVERT: A 14 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6811 (tt0) REVERT: A 16 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7506 (mtt90) REVERT: A 98 LYS cc_start: 0.7221 (mttt) cc_final: 0.5872 (tttp) REVERT: B 39 ASP cc_start: 0.8156 (t70) cc_final: 0.7832 (t0) REVERT: B 74 ARG cc_start: 0.6930 (mtt90) cc_final: 0.5938 (mtt180) REVERT: B 98 LYS cc_start: 0.7837 (mttt) cc_final: 0.7478 (mtmt) REVERT: B 122 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7780 (tp30) REVERT: B 133 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7128 (tt) REVERT: C 98 LYS cc_start: 0.7451 (mttt) cc_final: 0.6165 (tttp) REVERT: C 112 TYR cc_start: 0.8477 (m-80) cc_final: 0.8044 (m-80) REVERT: C 122 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6781 (tt0) REVERT: D 74 ARG cc_start: 0.7292 (mtt90) cc_final: 0.6308 (mtt180) REVERT: D 98 LYS cc_start: 0.8000 (mttt) cc_final: 0.7754 (mtmt) REVERT: E 20 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7476 (mtm180) REVERT: F 14 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7522 (tp30) REVERT: F 33 ARG cc_start: 0.8666 (mmm160) cc_final: 0.6336 (mmt90) REVERT: F 39 ASP cc_start: 0.8108 (t70) cc_final: 0.7708 (t0) REVERT: F 74 ARG cc_start: 0.7423 (mtt90) cc_final: 0.6500 (mtt180) REVERT: F 98 LYS cc_start: 0.7996 (mttt) cc_final: 0.7375 (ttpt) outliers start: 23 outliers final: 20 residues processed: 139 average time/residue: 0.1321 time to fit residues: 21.8136 Evaluate side-chains 147 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120028 restraints weight = 7756.217| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.48 r_work: 0.3398 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6294 Z= 0.147 Angle : 0.684 5.552 8508 Z= 0.359 Chirality : 0.052 0.149 882 Planarity : 0.004 0.044 1116 Dihedral : 7.733 89.443 876 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.85 % Allowed : 18.17 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 16 TYR 0.014 0.002 TYR D 86 PHE 0.022 0.002 PHE B 85 TRP 0.002 0.001 TRP E 3 HIS 0.011 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 6276) covalent geometry : angle 0.68227 / 0.36 ( 8472) SS BOND : bond 0.00288 / 0.16 ( 18) SS BOND : angle 1.08419 / 0.82 ( 36) hydrogen bonds : bond 0.02381 / 1.61 ( 86) hydrogen bonds : angle 5.79762 / 4.13 ( 258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.189 Fit side-chains REVERT: A 14 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6802 (tt0) REVERT: A 16 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7581 (mtt90) REVERT: A 88 LYS cc_start: 0.7579 (ttmt) cc_final: 0.7243 (mtmt) REVERT: A 98 LYS cc_start: 0.7250 (mttt) cc_final: 0.5967 (tmtt) REVERT: B 33 ARG cc_start: 0.8675 (mtp85) cc_final: 0.7017 (mpt180) REVERT: B 39 ASP cc_start: 0.8167 (t70) cc_final: 0.7864 (t0) REVERT: B 74 ARG cc_start: 0.6888 (mtt90) cc_final: 0.5959 (mtt180) REVERT: B 98 LYS cc_start: 0.7836 (mttt) cc_final: 0.7633 (mtmt) REVERT: B 122 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: B 133 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7160 (tt) REVERT: C 98 LYS cc_start: 0.7468 (mttt) cc_final: 0.6257 (tttp) REVERT: C 112 TYR cc_start: 0.8391 (m-80) cc_final: 0.7992 (m-80) REVERT: C 122 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: D 39 ASP cc_start: 0.8290 (t70) cc_final: 0.8029 (t0) REVERT: D 74 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6329 (mtt180) REVERT: D 98 LYS cc_start: 0.7994 (mttt) cc_final: 0.7729 (mtmt) REVERT: E 20 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7457 (mtm180) REVERT: E 88 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7628 (mtmt) REVERT: F 14 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7500 (tp30) REVERT: F 74 ARG cc_start: 0.7426 (mtt90) cc_final: 0.6565 (mtt180) REVERT: F 98 LYS cc_start: 0.7975 (mttt) cc_final: 0.7656 (mttm) outliers start: 19 outliers final: 15 residues processed: 139 average time/residue: 0.1393 time to fit residues: 23.0039 Evaluate side-chains 144 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 9.9990 chunk 42 optimal weight: 0.0470 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 70 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 1.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124893 restraints weight = 7670.016| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.40 r_work: 0.3469 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6294 Z= 0.102 Angle : 0.616 5.202 8508 Z= 0.324 Chirality : 0.051 0.146 882 Planarity : 0.004 0.043 1116 Dihedral : 7.422 87.205 876 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 1.65 % Allowed : 19.37 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 16 TYR 0.013 0.001 TYR D 86 PHE 0.018 0.001 PHE D 85 TRP 0.002 0.000 TRP F 3 HIS 0.007 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 6276) covalent geometry : angle 0.61432 / 0.32 ( 8472) SS BOND : bond 0.00235 / 0.15 ( 18) SS BOND : angle 0.94244 / 0.72 ( 36) hydrogen bonds : bond 0.02098 / 1.41 ( 86) hydrogen bonds : angle 5.50567 / 3.95 ( 258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6962 (tt0) REVERT: A 59 GLN cc_start: 0.8402 (mp-120) cc_final: 0.8142 (mp-120) REVERT: A 88 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7391 (mttt) REVERT: A 98 LYS cc_start: 0.7294 (mttt) cc_final: 0.6014 (tttp) REVERT: B 33 ARG cc_start: 0.8546 (mtp85) cc_final: 0.6938 (mpt180) REVERT: B 39 ASP cc_start: 0.8148 (t70) cc_final: 0.7874 (t0) REVERT: B 74 ARG cc_start: 0.6826 (mtt90) cc_final: 0.6035 (mtt180) REVERT: B 98 LYS cc_start: 0.7963 (mttt) cc_final: 0.7734 (mtmt) REVERT: B 122 GLU cc_start: 0.7967 (tt0) cc_final: 0.7581 (tp30) REVERT: B 133 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7155 (tt) REVERT: C 14 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6850 (tt0) REVERT: C 98 LYS cc_start: 0.7451 (mttt) cc_final: 0.6248 (tttp) REVERT: C 112 TYR cc_start: 0.8302 (m-80) cc_final: 0.7935 (m-80) REVERT: C 122 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6792 (tt0) REVERT: D 39 ASP cc_start: 0.8252 (t70) cc_final: 0.8012 (t0) REVERT: D 74 ARG cc_start: 0.7230 (mtt90) cc_final: 0.6361 (mtt180) REVERT: E 14 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6706 (tt0) REVERT: E 20 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7598 (mtm180) REVERT: E 88 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7605 (mtmt) REVERT: F 14 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7392 (tp30) REVERT: F 74 ARG cc_start: 0.7391 (mtt90) cc_final: 0.6684 (mtt180) REVERT: F 98 LYS cc_start: 0.7964 (mttt) cc_final: 0.7634 (mttm) outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.1333 time to fit residues: 21.6801 Evaluate side-chains 137 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 chunk 44 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 69 optimal weight: 0.0040 chunk 28 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123657 restraints weight = 7709.330| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.53 r_work: 0.3457 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6294 Z= 0.110 Angle : 0.630 6.218 8508 Z= 0.329 Chirality : 0.051 0.144 882 Planarity : 0.004 0.043 1116 Dihedral : 7.415 86.602 876 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 1.65 % Allowed : 19.82 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 16 TYR 0.013 0.002 TYR D 86 PHE 0.019 0.002 PHE D 85 TRP 0.001 0.000 TRP B 3 HIS 0.009 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 6276) covalent geometry : angle 0.62808 / 0.33 ( 8472) SS BOND : bond 0.00245 / 0.15 ( 18) SS BOND : angle 0.98846 / 0.76 ( 36) hydrogen bonds : bond 0.02107 / 1.42 ( 86) hydrogen bonds : angle 5.46268 / 3.91 ( 258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.25 seconds wall clock time: 30 minutes 32.17 seconds (1832.17 seconds total)