Starting phenix.real_space_refine on Sun Jul 27 21:36:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vx4_21429/07_2025/6vx4_21429.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx4_21429/07_2025/6vx4_21429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vx4_21429/07_2025/6vx4_21429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx4_21429/07_2025/6vx4_21429.map" model { file = "/net/cci-nas-00/data/ceres_data/6vx4_21429/07_2025/6vx4_21429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx4_21429/07_2025/6vx4_21429.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 41 5.16 5 C 6239 2.51 5 N 1659 2.21 5 O 1874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9813 Number of models: 1 Model: "" Number of chains: 9 Chain: "K" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 781 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1769 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain: "F" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1908 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 14, 'TRANS': 232} Time building chain proxies: 5.80, per 1000 atoms: 0.59 Number of scatterers: 9813 At special positions: 0 Unit cell: (83.64, 86.1, 136.53, 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 41 16.00 O 1874 8.00 N 1659 7.00 C 6239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 133 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 133 " distance=2.03 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 214 " - pdb=" SG CYS F 269 " distance=2.03 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 19.8% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.717A pdb=" N ASP C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.667A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.906A pdb=" N ASP A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 96 removed outlier: 3.770A pdb=" N ASP B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.601A pdb=" N ASP D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 81 through 96 removed outlier: 3.548A pdb=" N ASP E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR E 91 " --> pdb=" O ASP E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 117 Processing helix chain 'G' and resid 29 through 37 Processing helix chain 'G' and resid 46 through 52 removed outlier: 3.508A pdb=" N SER G 52 " --> pdb=" O GLN G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 84 removed outlier: 3.652A pdb=" N THR G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 121 through 132 Processing helix chain 'G' and resid 207 through 213 removed outlier: 6.711A pdb=" N ILE G 210 " --> pdb=" O CYS G 207 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLY G 211 " --> pdb=" O PHE G 208 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL G 213 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 241 removed outlier: 3.631A pdb=" N SER G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 47 through 54 removed outlier: 3.555A pdb=" N GLN F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 181 removed outlier: 3.715A pdb=" N THR F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 207 Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.525A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.564A pdb=" N SER K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU K 33 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 32 through 46 removed outlier: 4.928A pdb=" N TYR C 33 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 103 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C 35 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 101 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU C 125 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS C 102 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 122 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N CYS C 70 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLY C 124 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 12.787A pdb=" N VAL C 72 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 16.935A pdb=" N SER C 126 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 58 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE C 39 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN C 46 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N VAL E 123 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE E 101 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER E 35 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL E 103 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR E 33 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 121 through 126 removed outlier: 8.545A pdb=" N VAL C 123 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 46 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS A 56 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 42 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS A 54 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 44 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A 52 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 46 removed outlier: 5.113A pdb=" N TYR A 33 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 103 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER A 35 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 101 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG A 100 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU A 125 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS A 102 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL A 123 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 46 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE B 39 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 58 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 46 removed outlier: 4.856A pdb=" N TYR B 33 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 103 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER B 35 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 101 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 100 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU B 125 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS B 102 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N VAL B 123 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN D 46 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE D 39 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 58 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 32 through 46 removed outlier: 5.368A pdb=" N TYR D 33 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 103 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER D 35 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE D 101 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 124 " --> pdb=" O HIS D 102 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL D 123 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 46 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS E 56 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU E 42 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS E 54 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL E 44 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR E 52 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.653A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.563A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE H 59 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.540A pdb=" N PHE H 33 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 21 through 22 removed outlier: 3.969A pdb=" N LEU G 92 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 147 " --> pdb=" O GLN G 96 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG G 98 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE G 145 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 25 through 26 removed outlier: 3.549A pdb=" N ASP G 26 " --> pdb=" O TYR G 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR G 93 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU G 92 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 147 " --> pdb=" O GLN G 96 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG G 98 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE G 145 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 103 through 105 Processing sheet with id=AB5, first strand: chain 'G' and resid 204 through 205 Processing sheet with id=AB6, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.582A pdb=" N ASP F 91 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET F 30 " --> pdb=" O MET F 63 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLN F 65 " --> pdb=" O MET F 30 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TRP F 32 " --> pdb=" O GLN F 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 85 removed outlier: 5.616A pdb=" N PHE F 84 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 147 " --> pdb=" O THR F 158 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP F 190 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL F 238 " --> pdb=" O TRP F 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR F 234 " --> pdb=" O GLY F 194 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3152 1.34 - 1.46: 2429 1.46 - 1.58: 4424 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 10059 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" CA TYR G 95 " pdb=" C TYR G 95 " ideal model delta sigma weight residual 1.526 1.513 0.013 1.22e-02 6.72e+03 1.09e+00 bond pdb=" CA ILE F 88 " pdb=" CB ILE F 88 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 1.02e+00 bond pdb=" CA ILE G 197 " pdb=" CB ILE G 197 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.73e-01 bond pdb=" N PHE A 117 " pdb=" CA PHE A 117 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 7.32e-01 ... (remaining 10054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 13432 1.17 - 2.34: 201 2.34 - 3.51: 44 3.51 - 4.68: 23 4.68 - 5.84: 2 Bond angle restraints: 13702 Sorted by residual: angle pdb=" N TYR G 95 " pdb=" CA TYR G 95 " pdb=" C TYR G 95 " ideal model delta sigma weight residual 107.57 113.41 -5.84 1.94e+00 2.66e-01 9.08e+00 angle pdb=" C TRP C 78 " pdb=" N ALA C 79 " pdb=" CA ALA C 79 " ideal model delta sigma weight residual 119.78 123.20 -3.42 1.24e+00 6.50e-01 7.60e+00 angle pdb=" N ILE H 30 " pdb=" CA ILE H 30 " pdb=" C ILE H 30 " ideal model delta sigma weight residual 112.98 110.27 2.71 1.25e+00 6.40e-01 4.70e+00 angle pdb=" N LEU G 92 " pdb=" CA LEU G 92 " pdb=" C LEU G 92 " ideal model delta sigma weight residual 108.13 111.78 -3.65 1.72e+00 3.38e-01 4.51e+00 angle pdb=" CA LYS H 13 " pdb=" C LYS H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 117.69 119.49 -1.80 9.30e-01 1.16e+00 3.75e+00 ... (remaining 13697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5483 17.82 - 35.64: 342 35.64 - 53.45: 76 53.45 - 71.27: 14 71.27 - 89.09: 11 Dihedral angle restraints: 5926 sinusoidal: 2246 harmonic: 3680 Sorted by residual: dihedral pdb=" CB GLU F 223 " pdb=" CG GLU F 223 " pdb=" CD GLU F 223 " pdb=" OE1 GLU F 223 " ideal model delta sinusoidal sigma weight residual 0.00 -89.09 89.09 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 24 " pdb=" CG GLU E 24 " pdb=" CD GLU E 24 " pdb=" OE1 GLU E 24 " ideal model delta sinusoidal sigma weight residual 0.00 87.10 -87.10 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA ASP D 28 " pdb=" CB ASP D 28 " pdb=" CG ASP D 28 " pdb=" OD1 ASP D 28 " ideal model delta sinusoidal sigma weight residual -30.00 -83.07 53.07 1 2.00e+01 2.50e-03 9.58e+00 ... (remaining 5923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 938 0.029 - 0.059: 374 0.059 - 0.088: 93 0.088 - 0.117: 103 0.117 - 0.147: 13 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA VAL F 115 " pdb=" N VAL F 115 " pdb=" C VAL F 115 " pdb=" CB VAL F 115 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA TYR G 95 " pdb=" N TYR G 95 " pdb=" C TYR G 95 " pdb=" CB TYR G 95 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE G 66 " pdb=" N ILE G 66 " pdb=" C ILE G 66 " pdb=" CB ILE G 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1518 not shown) Planarity restraints: 1756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO H 14 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 15 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO H 16 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 16 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 16 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 95 " 0.012 2.00e-02 2.50e+03 7.24e-03 1.05e+00 pdb=" CG TYR G 95 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR G 95 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR G 95 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 95 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 95 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 95 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 95 " 0.004 2.00e-02 2.50e+03 ... (remaining 1753 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 594 2.72 - 3.26: 11004 3.26 - 3.81: 17721 3.81 - 4.35: 23220 4.35 - 4.90: 38368 Nonbonded interactions: 90907 Sorted by model distance: nonbonded pdb=" O SER H 75 " pdb=" OG SER H 76 " model vdw 2.173 3.040 nonbonded pdb=" OE1 GLN C 97 " pdb=" OH TYR A 93 " model vdw 2.211 3.040 nonbonded pdb=" O TRP K 92 " pdb=" NH1 ARG F 186 " model vdw 2.215 3.120 nonbonded pdb=" O ARG D 100 " pdb=" OG SER D 126 " model vdw 2.226 3.040 nonbonded pdb=" O TRP E 25 " pdb=" ND2 ASN E 31 " model vdw 2.233 3.120 ... (remaining 90902 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.950 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.002 0.033 10073 Z= 0.107 Angle : 0.433 5.845 13730 Z= 0.244 Chirality : 0.042 0.147 1521 Planarity : 0.002 0.050 1756 Dihedral : 12.959 89.090 3530 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.38 % Allowed : 7.22 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.19), residues: 1247 helix: -3.83 (0.22), residues: 213 sheet: -3.00 (0.21), residues: 411 loop : -2.91 (0.21), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS F 259 PHE 0.005 0.001 PHE G 185 TYR 0.016 0.001 TYR G 95 ARG 0.002 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.26272 ( 330) hydrogen bonds : angle 11.12039 ( 906) SS BOND : bond 0.00087 ( 14) SS BOND : angle 0.30336 ( 28) covalent geometry : bond 0.00211 (10059) covalent geometry : angle 0.43350 (13702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ASP cc_start: 0.6372 (t0) cc_final: 0.6155 (t0) REVERT: H 52 ASP cc_start: 0.7112 (t0) cc_final: 0.6618 (t0) REVERT: H 94 TYR cc_start: 0.7921 (m-80) cc_final: 0.7644 (m-80) REVERT: H 108 TYR cc_start: 0.8311 (m-80) cc_final: 0.7996 (m-80) REVERT: A 84 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5960 (mm-30) REVERT: A 103 VAL cc_start: 0.6957 (m) cc_final: 0.6527 (m) REVERT: B 87 ASP cc_start: 0.6558 (m-30) cc_final: 0.6157 (m-30) REVERT: D 58 VAL cc_start: 0.8789 (m) cc_final: 0.8539 (p) REVERT: D 86 LEU cc_start: 0.8372 (tp) cc_final: 0.8160 (tp) REVERT: D 91 TYR cc_start: 0.8332 (t80) cc_final: 0.8111 (t80) REVERT: E 58 VAL cc_start: 0.8072 (m) cc_final: 0.7860 (p) REVERT: E 83 LYS cc_start: 0.8191 (tptp) cc_final: 0.7441 (tptm) REVERT: G 20 ASP cc_start: 0.6930 (p0) cc_final: 0.6711 (p0) REVERT: G 227 MET cc_start: 0.7469 (tpp) cc_final: 0.7224 (tpp) REVERT: G 233 ARG cc_start: 0.7224 (mtm180) cc_final: 0.6753 (mtm-85) REVERT: F 34 LEU cc_start: 0.5580 (mt) cc_final: 0.4987 (mt) outliers start: 4 outliers final: 3 residues processed: 424 average time/residue: 0.2239 time to fit residues: 130.3209 Evaluate side-chains 300 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 297 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 42 ASN C 97 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS A 61 ASN A 97 GLN B 115 ASN D 88 GLN E 88 GLN E 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.091246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077985 restraints weight = 23431.261| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.29 r_work: 0.3368 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10073 Z= 0.288 Angle : 0.743 7.246 13730 Z= 0.397 Chirality : 0.051 0.224 1521 Planarity : 0.007 0.165 1756 Dihedral : 4.963 22.235 1381 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.94 % Allowed : 17.07 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.22), residues: 1247 helix: -1.35 (0.31), residues: 215 sheet: -2.30 (0.22), residues: 420 loop : -1.94 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 25 HIS 0.014 0.002 HIS F 160 PHE 0.025 0.003 PHE F 156 TYR 0.019 0.002 TYR A 52 ARG 0.006 0.001 ARG F 186 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 330) hydrogen bonds : angle 7.08976 ( 906) SS BOND : bond 0.00702 ( 14) SS BOND : angle 0.84296 ( 28) covalent geometry : bond 0.00636 (10059) covalent geometry : angle 0.74290 (13702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 335 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 23 LYS cc_start: 0.9223 (tptp) cc_final: 0.8816 (tptp) REVERT: H 31 ASP cc_start: 0.7056 (t0) cc_final: 0.6764 (t0) REVERT: H 38 MET cc_start: 0.7577 (tmm) cc_final: 0.7218 (ttt) REVERT: H 108 TYR cc_start: 0.8933 (m-80) cc_final: 0.8515 (m-80) REVERT: A 33 TYR cc_start: 0.8896 (p90) cc_final: 0.8591 (p90) REVERT: A 36 ASP cc_start: 0.8013 (m-30) cc_final: 0.7340 (t0) REVERT: A 83 LYS cc_start: 0.9009 (pttt) cc_final: 0.8731 (tptt) REVERT: A 91 TYR cc_start: 0.8845 (t80) cc_final: 0.8504 (t80) REVERT: B 36 ASP cc_start: 0.7428 (t70) cc_final: 0.6924 (t0) REVERT: B 56 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7832 (ttpp) REVERT: B 59 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8164 (mmmt) REVERT: B 75 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7901 (mm110) REVERT: B 83 LYS cc_start: 0.8992 (tmtt) cc_final: 0.8046 (tptp) REVERT: B 87 ASP cc_start: 0.8686 (m-30) cc_final: 0.8352 (m-30) REVERT: B 109 THR cc_start: 0.8613 (m) cc_final: 0.8411 (p) REVERT: D 36 ASP cc_start: 0.8235 (t0) cc_final: 0.7984 (t0) REVERT: D 91 TYR cc_start: 0.8789 (t80) cc_final: 0.8580 (t80) REVERT: E 36 ASP cc_start: 0.7248 (t70) cc_final: 0.6896 (t0) REVERT: E 41 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8101 (mt-10) REVERT: E 56 LYS cc_start: 0.8710 (tttt) cc_final: 0.8371 (ttmt) REVERT: E 83 LYS cc_start: 0.9154 (tptp) cc_final: 0.8726 (tppt) REVERT: E 87 ASP cc_start: 0.8574 (m-30) cc_final: 0.8331 (m-30) REVERT: E 91 TYR cc_start: 0.8237 (t80) cc_final: 0.7973 (t80) REVERT: G 112 TYR cc_start: 0.8813 (t80) cc_final: 0.8344 (t80) REVERT: G 116 GLN cc_start: 0.7779 (tt0) cc_final: 0.6974 (tt0) REVERT: G 123 TYR cc_start: 0.8219 (m-80) cc_final: 0.7422 (m-10) REVERT: G 233 ARG cc_start: 0.8184 (mtm180) cc_final: 0.7882 (mtm110) REVERT: G 237 GLU cc_start: 0.7779 (tp30) cc_final: 0.7343 (tp30) REVERT: F 26 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7083 (m-30) REVERT: F 91 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8134 (p0) REVERT: F 93 TYR cc_start: 0.8496 (m-80) cc_final: 0.8160 (m-80) REVERT: F 157 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9289 (mp) REVERT: F 205 ASN cc_start: 0.8974 (t0) cc_final: 0.8589 (t0) outliers start: 42 outliers final: 23 residues processed: 352 average time/residue: 0.2193 time to fit residues: 106.9628 Evaluate side-chains 295 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN B 97 GLN B 104 GLN D 88 GLN D 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN G 116 GLN G 195 GLN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN F 128 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.091790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078676 restraints weight = 23695.551| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.25 r_work: 0.3386 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10073 Z= 0.174 Angle : 0.631 7.348 13730 Z= 0.332 Chirality : 0.048 0.192 1521 Planarity : 0.005 0.055 1756 Dihedral : 4.517 21.604 1378 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.00 % Allowed : 20.45 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.23), residues: 1247 helix: -0.46 (0.35), residues: 216 sheet: -1.76 (0.23), residues: 408 loop : -1.54 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 32 HIS 0.010 0.001 HIS F 259 PHE 0.019 0.002 PHE F 156 TYR 0.026 0.002 TYR D 33 ARG 0.016 0.001 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 330) hydrogen bonds : angle 6.19413 ( 906) SS BOND : bond 0.00357 ( 14) SS BOND : angle 0.67559 ( 28) covalent geometry : bond 0.00390 (10059) covalent geometry : angle 0.63052 (13702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 305 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 69 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8576 (mtmm) REVERT: K 82 ASP cc_start: 0.8634 (m-30) cc_final: 0.7506 (m-30) REVERT: K 92 TRP cc_start: 0.8664 (t-100) cc_final: 0.8434 (t-100) REVERT: C 36 ASP cc_start: 0.8526 (m-30) cc_final: 0.8015 (t0) REVERT: C 83 LYS cc_start: 0.8558 (tmtt) cc_final: 0.8328 (tmmt) REVERT: C 84 GLU cc_start: 0.7582 (mp0) cc_final: 0.7361 (mp0) REVERT: C 91 TYR cc_start: 0.8783 (t80) cc_final: 0.8378 (t80) REVERT: H 23 LYS cc_start: 0.9227 (tptp) cc_final: 0.8962 (tppp) REVERT: H 31 ASP cc_start: 0.6857 (t0) cc_final: 0.6576 (t0) REVERT: H 46 GLU cc_start: 0.8672 (pt0) cc_final: 0.8144 (pt0) REVERT: H 54 TYR cc_start: 0.8488 (t80) cc_final: 0.8267 (t80) REVERT: H 82 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8208 (mm-30) REVERT: H 107 ASP cc_start: 0.8436 (t0) cc_final: 0.8115 (t0) REVERT: H 108 TYR cc_start: 0.9041 (m-80) cc_final: 0.8348 (m-80) REVERT: A 36 ASP cc_start: 0.8080 (m-30) cc_final: 0.7818 (t70) REVERT: A 41 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6553 (mt-10) REVERT: A 91 TYR cc_start: 0.8961 (t80) cc_final: 0.8655 (t80) REVERT: B 36 ASP cc_start: 0.7285 (t70) cc_final: 0.7011 (t0) REVERT: B 37 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8283 (mm-30) REVERT: B 56 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7921 (tttm) REVERT: B 59 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8405 (mmmt) REVERT: B 75 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7806 (mm110) REVERT: B 83 LYS cc_start: 0.9025 (tmtt) cc_final: 0.8030 (tptp) REVERT: B 87 ASP cc_start: 0.8689 (m-30) cc_final: 0.8246 (m-30) REVERT: D 36 ASP cc_start: 0.8211 (t0) cc_final: 0.7963 (t0) REVERT: D 83 LYS cc_start: 0.9086 (tppt) cc_final: 0.8877 (tppp) REVERT: D 91 TYR cc_start: 0.8711 (t80) cc_final: 0.8436 (t80) REVERT: E 28 ASP cc_start: 0.7651 (m-30) cc_final: 0.7331 (m-30) REVERT: E 36 ASP cc_start: 0.7146 (t70) cc_final: 0.6887 (t70) REVERT: E 41 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7946 (mt-10) REVERT: E 56 LYS cc_start: 0.8721 (tttt) cc_final: 0.8437 (ttmt) REVERT: E 83 LYS cc_start: 0.9089 (tptp) cc_final: 0.8535 (tppt) REVERT: E 84 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8249 (mm-30) REVERT: E 87 ASP cc_start: 0.8659 (m-30) cc_final: 0.8320 (m-30) REVERT: E 88 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: E 104 GLN cc_start: 0.7535 (tt0) cc_final: 0.7327 (tt0) REVERT: E 110 TYR cc_start: 0.7983 (t80) cc_final: 0.7742 (t80) REVERT: G 85 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.7775 (mmm-85) REVERT: G 112 TYR cc_start: 0.8715 (t80) cc_final: 0.8307 (t80) REVERT: G 123 TYR cc_start: 0.8185 (m-80) cc_final: 0.7454 (m-10) REVERT: G 143 GLU cc_start: 0.8504 (mp0) cc_final: 0.8254 (mp0) REVERT: G 233 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7931 (mtm110) REVERT: G 237 GLU cc_start: 0.7638 (tp30) cc_final: 0.7158 (tp30) REVERT: F 26 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: F 91 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.7933 (p0) REVERT: F 93 TYR cc_start: 0.8513 (m-80) cc_final: 0.8089 (m-80) REVERT: F 204 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7648 (mt-10) REVERT: F 208 MET cc_start: 0.7189 (mmm) cc_final: 0.6928 (mmm) REVERT: F 213 GLU cc_start: 0.8154 (tp30) cc_final: 0.7607 (tp30) outliers start: 32 outliers final: 22 residues processed: 323 average time/residue: 0.2272 time to fit residues: 101.4080 Evaluate side-chains 297 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075191 restraints weight = 23818.435| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.32 r_work: 0.3315 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10073 Z= 0.219 Angle : 0.640 7.116 13730 Z= 0.333 Chirality : 0.048 0.201 1521 Planarity : 0.005 0.063 1756 Dihedral : 4.609 21.440 1378 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.50 % Allowed : 19.79 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.23), residues: 1247 helix: -0.13 (0.36), residues: 211 sheet: -1.54 (0.23), residues: 410 loop : -1.29 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 78 HIS 0.010 0.001 HIS F 259 PHE 0.021 0.002 PHE F 156 TYR 0.014 0.002 TYR G 95 ARG 0.014 0.001 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 330) hydrogen bonds : angle 6.06350 ( 906) SS BOND : bond 0.00325 ( 14) SS BOND : angle 0.61047 ( 28) covalent geometry : bond 0.00490 (10059) covalent geometry : angle 0.64035 (13702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 61 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7234 (ptt180) REVERT: K 69 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8683 (mtmm) REVERT: K 92 TRP cc_start: 0.8626 (t-100) cc_final: 0.8179 (t-100) REVERT: C 36 ASP cc_start: 0.8677 (m-30) cc_final: 0.8206 (t0) REVERT: H 23 LYS cc_start: 0.9297 (tptp) cc_final: 0.9072 (tppp) REVERT: H 31 ASP cc_start: 0.7015 (t0) cc_final: 0.6745 (t0) REVERT: H 36 TRP cc_start: 0.8851 (m100) cc_final: 0.8550 (m100) REVERT: H 38 MET cc_start: 0.8320 (ttt) cc_final: 0.7382 (ttt) REVERT: H 46 GLU cc_start: 0.8719 (pt0) cc_final: 0.8284 (pm20) REVERT: H 54 TYR cc_start: 0.8617 (t80) cc_final: 0.8392 (t80) REVERT: H 69 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8534 (p) REVERT: H 81 MET cc_start: 0.8726 (ttt) cc_final: 0.8304 (ttp) REVERT: H 107 ASP cc_start: 0.8361 (t0) cc_final: 0.8014 (t0) REVERT: H 108 TYR cc_start: 0.8958 (m-80) cc_final: 0.8225 (m-80) REVERT: A 41 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6724 (mt-10) REVERT: A 91 TYR cc_start: 0.8935 (t80) cc_final: 0.8641 (t80) REVERT: B 28 ASP cc_start: 0.7973 (m-30) cc_final: 0.7459 (m-30) REVERT: B 36 ASP cc_start: 0.7643 (t70) cc_final: 0.7348 (t0) REVERT: B 56 LYS cc_start: 0.8468 (ttmt) cc_final: 0.7845 (tttm) REVERT: B 75 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7727 (mm110) REVERT: B 83 LYS cc_start: 0.8966 (tmtt) cc_final: 0.7997 (tptp) REVERT: B 87 ASP cc_start: 0.8827 (m-30) cc_final: 0.8328 (m-30) REVERT: D 36 ASP cc_start: 0.8387 (t0) cc_final: 0.8163 (t0) REVERT: D 41 GLU cc_start: 0.8812 (mp0) cc_final: 0.8342 (mm-30) REVERT: D 91 TYR cc_start: 0.8816 (t80) cc_final: 0.8538 (t80) REVERT: E 28 ASP cc_start: 0.7886 (m-30) cc_final: 0.7386 (m-30) REVERT: E 41 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7593 (mt-10) REVERT: E 56 LYS cc_start: 0.8646 (tttt) cc_final: 0.8236 (ttpt) REVERT: E 83 LYS cc_start: 0.9118 (tptp) cc_final: 0.8743 (tppt) REVERT: E 88 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: E 110 TYR cc_start: 0.8046 (t80) cc_final: 0.7714 (t80) REVERT: G 188 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7812 (mm-30) REVERT: F 26 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: F 91 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.7815 (p0) REVERT: F 93 TYR cc_start: 0.8638 (m-80) cc_final: 0.8195 (m-80) REVERT: F 157 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9105 (mt) REVERT: F 185 MET cc_start: 0.9031 (mpp) cc_final: 0.8575 (mpp) REVERT: F 204 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7624 (mt-10) REVERT: F 208 MET cc_start: 0.7356 (mmm) cc_final: 0.6903 (mmm) REVERT: F 213 GLU cc_start: 0.8217 (tp30) cc_final: 0.7631 (tp30) REVERT: F 260 TYR cc_start: 0.8847 (m-80) cc_final: 0.8611 (m-10) outliers start: 48 outliers final: 30 residues processed: 312 average time/residue: 0.2249 time to fit residues: 97.3840 Evaluate side-chains 302 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 265 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 118 ARG Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 0.0070 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN D 88 GLN E 115 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.088194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.074944 restraints weight = 23743.899| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.26 r_work: 0.3310 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10073 Z= 0.196 Angle : 0.630 10.405 13730 Z= 0.323 Chirality : 0.048 0.217 1521 Planarity : 0.005 0.050 1756 Dihedral : 4.552 20.216 1378 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 5.16 % Allowed : 19.61 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.23), residues: 1247 helix: -0.15 (0.36), residues: 218 sheet: -1.26 (0.24), residues: 399 loop : -1.28 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 78 HIS 0.008 0.001 HIS F 259 PHE 0.018 0.002 PHE F 156 TYR 0.014 0.001 TYR G 123 ARG 0.013 0.001 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 330) hydrogen bonds : angle 5.92402 ( 906) SS BOND : bond 0.00379 ( 14) SS BOND : angle 0.67771 ( 28) covalent geometry : bond 0.00444 (10059) covalent geometry : angle 0.63022 (13702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7833 (tp) REVERT: C 36 ASP cc_start: 0.8565 (m-30) cc_final: 0.8118 (t0) REVERT: C 49 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8340 (p) REVERT: C 74 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8531 (mtmm) REVERT: C 91 TYR cc_start: 0.8960 (t80) cc_final: 0.8426 (t80) REVERT: H 31 ASP cc_start: 0.6921 (t0) cc_final: 0.6663 (t0) REVERT: H 37 VAL cc_start: 0.9215 (t) cc_final: 0.8961 (t) REVERT: H 38 MET cc_start: 0.8489 (ttt) cc_final: 0.7298 (ttt) REVERT: H 45 LEU cc_start: 0.9317 (mt) cc_final: 0.9057 (tp) REVERT: H 46 GLU cc_start: 0.8696 (pt0) cc_final: 0.8383 (pm20) REVERT: H 54 TYR cc_start: 0.8627 (t80) cc_final: 0.8398 (t80) REVERT: H 107 ASP cc_start: 0.8148 (t0) cc_final: 0.7780 (t0) REVERT: H 108 TYR cc_start: 0.8946 (m-80) cc_final: 0.8265 (m-80) REVERT: A 36 ASP cc_start: 0.8466 (m-30) cc_final: 0.7654 (t0) REVERT: A 41 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 91 TYR cc_start: 0.9051 (t80) cc_final: 0.8812 (t80) REVERT: B 28 ASP cc_start: 0.8069 (m-30) cc_final: 0.7587 (m-30) REVERT: B 36 ASP cc_start: 0.7730 (t70) cc_final: 0.7366 (t0) REVERT: B 56 LYS cc_start: 0.8468 (ttmt) cc_final: 0.7838 (tttm) REVERT: B 75 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7794 (mm110) REVERT: B 83 LYS cc_start: 0.8872 (tmtt) cc_final: 0.7948 (tptp) REVERT: B 87 ASP cc_start: 0.8834 (m-30) cc_final: 0.8355 (m-30) REVERT: B 117 PHE cc_start: 0.8116 (m-10) cc_final: 0.7849 (m-10) REVERT: D 36 ASP cc_start: 0.8382 (t0) cc_final: 0.8169 (t0) REVERT: D 41 GLU cc_start: 0.8810 (mp0) cc_final: 0.8364 (mm-30) REVERT: D 84 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: D 88 GLN cc_start: 0.8762 (tp40) cc_final: 0.8515 (tp-100) REVERT: D 91 TYR cc_start: 0.8821 (t80) cc_final: 0.8519 (t80) REVERT: E 28 ASP cc_start: 0.7911 (m-30) cc_final: 0.7467 (m-30) REVERT: E 41 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8036 (mt-10) REVERT: E 56 LYS cc_start: 0.8642 (tttt) cc_final: 0.8336 (ttmt) REVERT: E 83 LYS cc_start: 0.9102 (tptp) cc_final: 0.8797 (tppt) REVERT: E 84 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8281 (mm-30) REVERT: E 88 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8382 (mp10) REVERT: E 110 TYR cc_start: 0.8088 (t80) cc_final: 0.7710 (t80) REVERT: G 85 ARG cc_start: 0.8724 (mmm-85) cc_final: 0.7637 (mmm-85) REVERT: G 123 TYR cc_start: 0.8339 (m-10) cc_final: 0.8080 (m-10) REVERT: F 26 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: F 91 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.7999 (p0) REVERT: F 93 TYR cc_start: 0.8715 (m-80) cc_final: 0.8502 (m-80) REVERT: F 185 MET cc_start: 0.9059 (mpp) cc_final: 0.8578 (mpp) REVERT: F 213 GLU cc_start: 0.8248 (tp30) cc_final: 0.7596 (tp30) outliers start: 55 outliers final: 35 residues processed: 320 average time/residue: 0.1989 time to fit residues: 90.4225 Evaluate side-chains 311 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS H 5 GLN E 75 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.089691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076690 restraints weight = 23742.651| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.20 r_work: 0.3351 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.7046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10073 Z= 0.153 Angle : 0.625 10.330 13730 Z= 0.319 Chirality : 0.048 0.243 1521 Planarity : 0.004 0.044 1756 Dihedral : 4.444 20.341 1378 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.47 % Allowed : 22.51 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1247 helix: 0.14 (0.36), residues: 212 sheet: -1.14 (0.24), residues: 405 loop : -1.16 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 78 HIS 0.007 0.001 HIS F 259 PHE 0.017 0.002 PHE D 113 TYR 0.017 0.001 TYR H 27 ARG 0.009 0.001 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 330) hydrogen bonds : angle 5.76648 ( 906) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.56953 ( 28) covalent geometry : bond 0.00352 (10059) covalent geometry : angle 0.62539 (13702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8608 (t) cc_final: 0.7536 (t) REVERT: C 36 ASP cc_start: 0.8637 (m-30) cc_final: 0.8236 (t0) REVERT: C 37 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8108 (mm-30) REVERT: C 74 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8528 (mtmm) REVERT: C 82 PHE cc_start: 0.8584 (t80) cc_final: 0.8053 (t80) REVERT: C 90 ARG cc_start: 0.8719 (ttm110) cc_final: 0.8469 (ttm110) REVERT: C 91 TYR cc_start: 0.8899 (t80) cc_final: 0.8467 (t80) REVERT: H 31 ASP cc_start: 0.6810 (t0) cc_final: 0.6536 (t0) REVERT: H 38 MET cc_start: 0.8461 (ttt) cc_final: 0.7197 (ttt) REVERT: H 46 GLU cc_start: 0.8662 (pt0) cc_final: 0.8412 (pm20) REVERT: H 54 TYR cc_start: 0.8630 (t80) cc_final: 0.8395 (t80) REVERT: H 81 MET cc_start: 0.8563 (ttt) cc_final: 0.8152 (ttp) REVERT: H 107 ASP cc_start: 0.8023 (t0) cc_final: 0.7573 (t0) REVERT: H 108 TYR cc_start: 0.8796 (m-80) cc_final: 0.8060 (m-80) REVERT: A 36 ASP cc_start: 0.8265 (m-30) cc_final: 0.7939 (t0) REVERT: A 41 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6952 (mt-10) REVERT: A 91 TYR cc_start: 0.9036 (t80) cc_final: 0.8779 (t80) REVERT: B 28 ASP cc_start: 0.7842 (m-30) cc_final: 0.7393 (m-30) REVERT: B 36 ASP cc_start: 0.7544 (t70) cc_final: 0.7279 (t70) REVERT: B 56 LYS cc_start: 0.8482 (ttmt) cc_final: 0.7863 (tttm) REVERT: B 75 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7773 (mm110) REVERT: B 83 LYS cc_start: 0.8872 (tmtt) cc_final: 0.7970 (tptp) REVERT: B 87 ASP cc_start: 0.8814 (m-30) cc_final: 0.8322 (m-30) REVERT: D 91 TYR cc_start: 0.8768 (t80) cc_final: 0.8484 (t80) REVERT: E 24 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: E 28 ASP cc_start: 0.7935 (m-30) cc_final: 0.7521 (m-30) REVERT: E 41 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7930 (mt-10) REVERT: E 56 LYS cc_start: 0.8627 (tttt) cc_final: 0.8250 (ttpt) REVERT: E 75 GLN cc_start: 0.7942 (mm110) cc_final: 0.7705 (mp10) REVERT: E 83 LYS cc_start: 0.9064 (tptp) cc_final: 0.8779 (tppt) REVERT: E 88 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: E 110 TYR cc_start: 0.8199 (t80) cc_final: 0.7765 (t80) REVERT: F 26 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: F 91 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.7776 (p0) REVERT: F 93 TYR cc_start: 0.8631 (m-80) cc_final: 0.8150 (m-80) REVERT: F 185 MET cc_start: 0.8996 (mpp) cc_final: 0.8521 (mpp) REVERT: F 213 GLU cc_start: 0.8241 (tp30) cc_final: 0.7463 (tp30) outliers start: 37 outliers final: 27 residues processed: 315 average time/residue: 0.2287 time to fit residues: 103.7470 Evaluate side-chains 303 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 271 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS C 75 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN D 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.090534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.076707 restraints weight = 24255.499| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.44 r_work: 0.3360 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10073 Z= 0.146 Angle : 0.637 10.656 13730 Z= 0.327 Chirality : 0.049 0.324 1521 Planarity : 0.005 0.061 1756 Dihedral : 4.425 20.049 1378 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.28 % Allowed : 23.17 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1247 helix: 0.31 (0.36), residues: 212 sheet: -1.19 (0.24), residues: 405 loop : -1.03 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 78 HIS 0.007 0.001 HIS F 259 PHE 0.017 0.002 PHE D 113 TYR 0.030 0.001 TYR F 260 ARG 0.008 0.001 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 330) hydrogen bonds : angle 5.70187 ( 906) SS BOND : bond 0.00244 ( 14) SS BOND : angle 0.86040 ( 28) covalent geometry : bond 0.00340 (10059) covalent geometry : angle 0.63680 (13702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7830 (tp) REVERT: K 49 SER cc_start: 0.8724 (t) cc_final: 0.7544 (t) REVERT: K 69 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8354 (mmmm) REVERT: C 33 TYR cc_start: 0.8361 (p90) cc_final: 0.8147 (p90) REVERT: C 36 ASP cc_start: 0.8605 (m-30) cc_final: 0.8224 (t0) REVERT: C 37 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8084 (mm-30) REVERT: C 74 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8536 (mtmm) REVERT: C 82 PHE cc_start: 0.8469 (t80) cc_final: 0.7903 (t80) REVERT: C 90 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8479 (ttm110) REVERT: C 91 TYR cc_start: 0.8936 (t80) cc_final: 0.8490 (t80) REVERT: H 4 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8459 (mm) REVERT: H 31 ASP cc_start: 0.6803 (t0) cc_final: 0.6499 (t0) REVERT: H 36 TRP cc_start: 0.8670 (m100) cc_final: 0.7616 (m100) REVERT: H 38 MET cc_start: 0.8658 (ttt) cc_final: 0.7333 (ttm) REVERT: H 46 GLU cc_start: 0.8619 (pt0) cc_final: 0.8306 (pm20) REVERT: H 54 TYR cc_start: 0.8688 (t80) cc_final: 0.8448 (t80) REVERT: H 81 MET cc_start: 0.8507 (ttt) cc_final: 0.8154 (ttp) REVERT: H 106 MET cc_start: 0.8218 (mmm) cc_final: 0.6694 (mmt) REVERT: H 107 ASP cc_start: 0.8034 (t0) cc_final: 0.7527 (t0) REVERT: H 108 TYR cc_start: 0.8730 (m-80) cc_final: 0.7941 (m-80) REVERT: A 36 ASP cc_start: 0.8278 (m-30) cc_final: 0.7927 (t0) REVERT: A 41 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6938 (mt-10) REVERT: A 75 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7987 (tp40) REVERT: A 91 TYR cc_start: 0.9019 (t80) cc_final: 0.8760 (t80) REVERT: B 36 ASP cc_start: 0.7770 (t70) cc_final: 0.7492 (t70) REVERT: B 56 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7737 (tttm) REVERT: B 75 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7842 (mm110) REVERT: B 83 LYS cc_start: 0.8904 (tmtt) cc_final: 0.8199 (tptp) REVERT: B 87 ASP cc_start: 0.8796 (m-30) cc_final: 0.8283 (m-30) REVERT: B 117 PHE cc_start: 0.8042 (m-10) cc_final: 0.7747 (m-10) REVERT: D 84 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: D 91 TYR cc_start: 0.8738 (t80) cc_final: 0.8503 (t80) REVERT: E 28 ASP cc_start: 0.7976 (m-30) cc_final: 0.7550 (m-30) REVERT: E 41 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7849 (mt-10) REVERT: E 56 LYS cc_start: 0.8641 (tttt) cc_final: 0.8248 (ttpt) REVERT: E 78 TRP cc_start: 0.7812 (m100) cc_final: 0.7460 (m100) REVERT: E 83 LYS cc_start: 0.9103 (tptp) cc_final: 0.8777 (tppt) REVERT: E 84 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7679 (mm-30) REVERT: E 87 ASP cc_start: 0.8705 (m-30) cc_final: 0.8499 (m-30) REVERT: E 88 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: E 110 TYR cc_start: 0.8137 (t80) cc_final: 0.7671 (t80) REVERT: G 85 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.7745 (mmm-85) REVERT: G 237 GLU cc_start: 0.7534 (tp30) cc_final: 0.7169 (tp30) REVERT: F 26 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: F 91 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.7885 (p0) REVERT: F 93 TYR cc_start: 0.8729 (m-80) cc_final: 0.8279 (m-80) REVERT: F 185 MET cc_start: 0.8968 (mpp) cc_final: 0.8439 (mpp) REVERT: F 204 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8190 (mt-10) REVERT: F 213 GLU cc_start: 0.8189 (tp30) cc_final: 0.7427 (tp30) REVERT: F 223 GLU cc_start: 0.8179 (pt0) cc_final: 0.7665 (pt0) REVERT: F 260 TYR cc_start: 0.8808 (m-10) cc_final: 0.8598 (m-10) outliers start: 35 outliers final: 20 residues processed: 307 average time/residue: 0.2048 time to fit residues: 89.1742 Evaluate side-chains 301 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 109 optimal weight: 0.0980 chunk 95 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS H 5 GLN D 88 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.092646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.079063 restraints weight = 23892.338| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.44 r_work: 0.3394 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.7430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10073 Z= 0.143 Angle : 0.664 11.473 13730 Z= 0.339 Chirality : 0.048 0.214 1521 Planarity : 0.005 0.074 1756 Dihedral : 4.417 20.694 1378 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.47 % Allowed : 23.83 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1247 helix: 0.03 (0.36), residues: 211 sheet: -1.02 (0.24), residues: 400 loop : -1.06 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 78 HIS 0.008 0.001 HIS K 28 PHE 0.027 0.002 PHE A 53 TYR 0.020 0.001 TYR F 260 ARG 0.004 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 330) hydrogen bonds : angle 5.69963 ( 906) SS BOND : bond 0.00230 ( 14) SS BOND : angle 0.89940 ( 28) covalent geometry : bond 0.00331 (10059) covalent geometry : angle 0.66389 (13702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8650 (t) cc_final: 0.7324 (t) REVERT: K 54 LEU cc_start: 0.8763 (tp) cc_final: 0.8522 (tp) REVERT: K 69 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8438 (mmmm) REVERT: C 33 TYR cc_start: 0.8383 (p90) cc_final: 0.8124 (p90) REVERT: C 36 ASP cc_start: 0.8505 (m-30) cc_final: 0.8131 (t0) REVERT: C 37 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8021 (mm-30) REVERT: C 74 LYS cc_start: 0.9029 (mtmm) cc_final: 0.8508 (mtmm) REVERT: C 82 PHE cc_start: 0.8418 (t80) cc_final: 0.8181 (t80) REVERT: C 91 TYR cc_start: 0.8963 (t80) cc_final: 0.8496 (t80) REVERT: C 93 TYR cc_start: 0.8690 (t80) cc_final: 0.8388 (t80) REVERT: H 4 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8470 (mm) REVERT: H 31 ASP cc_start: 0.6869 (t0) cc_final: 0.6635 (t0) REVERT: H 38 MET cc_start: 0.8572 (ttt) cc_final: 0.7336 (ttm) REVERT: H 46 GLU cc_start: 0.8675 (pt0) cc_final: 0.8413 (pm20) REVERT: H 54 TYR cc_start: 0.8595 (t80) cc_final: 0.8352 (t80) REVERT: H 106 MET cc_start: 0.8229 (mmm) cc_final: 0.7826 (mtt) REVERT: H 107 ASP cc_start: 0.8022 (t0) cc_final: 0.7492 (t0) REVERT: H 108 TYR cc_start: 0.8808 (m-80) cc_final: 0.8078 (m-80) REVERT: A 36 ASP cc_start: 0.8158 (m-30) cc_final: 0.7868 (t0) REVERT: A 41 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 75 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7988 (tp40) REVERT: A 91 TYR cc_start: 0.9045 (t80) cc_final: 0.8794 (t80) REVERT: A 132 GLN cc_start: 0.8313 (tt0) cc_final: 0.8061 (pt0) REVERT: B 56 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8101 (ttpp) REVERT: B 75 GLN cc_start: 0.8121 (tp40) cc_final: 0.7764 (mm110) REVERT: B 83 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8228 (tptp) REVERT: B 87 ASP cc_start: 0.8906 (m-30) cc_final: 0.8399 (m-30) REVERT: D 84 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: E 24 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: E 28 ASP cc_start: 0.8054 (m-30) cc_final: 0.7701 (m-30) REVERT: E 34 TYR cc_start: 0.8425 (m-80) cc_final: 0.8209 (m-80) REVERT: E 41 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7809 (mt-10) REVERT: E 56 LYS cc_start: 0.8678 (tttt) cc_final: 0.8281 (ttpt) REVERT: E 78 TRP cc_start: 0.7612 (m100) cc_final: 0.7403 (m100) REVERT: E 83 LYS cc_start: 0.9049 (tptp) cc_final: 0.8736 (tppt) REVERT: E 87 ASP cc_start: 0.8644 (m-30) cc_final: 0.8343 (m-30) REVERT: E 88 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8289 (mp10) REVERT: E 110 TYR cc_start: 0.8123 (t80) cc_final: 0.7600 (t80) REVERT: G 85 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.7811 (mmm-85) REVERT: G 123 TYR cc_start: 0.8298 (m-10) cc_final: 0.7807 (m-10) REVERT: F 26 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: F 91 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.7820 (p0) REVERT: F 93 TYR cc_start: 0.8610 (m-80) cc_final: 0.8334 (m-80) REVERT: F 185 MET cc_start: 0.9022 (mpp) cc_final: 0.8509 (mpp) REVERT: F 208 MET cc_start: 0.6819 (mmm) cc_final: 0.6513 (mmm) REVERT: F 213 GLU cc_start: 0.8147 (tp30) cc_final: 0.7283 (tp30) REVERT: F 223 GLU cc_start: 0.8142 (pt0) cc_final: 0.7657 (pt0) REVERT: F 248 GLU cc_start: 0.7122 (pm20) cc_final: 0.6844 (mp0) REVERT: F 260 TYR cc_start: 0.8766 (m-10) cc_final: 0.8334 (m-10) outliers start: 37 outliers final: 21 residues processed: 305 average time/residue: 0.2388 time to fit residues: 103.1120 Evaluate side-chains 294 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 115 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS H 5 GLN D 88 GLN D 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.091255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077975 restraints weight = 24118.025| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.34 r_work: 0.3380 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10073 Z= 0.150 Angle : 0.670 11.027 13730 Z= 0.343 Chirality : 0.048 0.217 1521 Planarity : 0.005 0.063 1756 Dihedral : 4.404 20.714 1378 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.72 % Allowed : 24.77 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.24), residues: 1247 helix: 0.17 (0.36), residues: 215 sheet: -0.98 (0.24), residues: 412 loop : -1.00 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 78 HIS 0.006 0.001 HIS F 259 PHE 0.026 0.002 PHE A 53 TYR 0.017 0.001 TYR F 260 ARG 0.012 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 330) hydrogen bonds : angle 5.63837 ( 906) SS BOND : bond 0.00242 ( 14) SS BOND : angle 0.81374 ( 28) covalent geometry : bond 0.00349 (10059) covalent geometry : angle 0.67014 (13702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8683 (t) cc_final: 0.7357 (t) REVERT: K 54 LEU cc_start: 0.8763 (tp) cc_final: 0.8542 (tp) REVERT: K 69 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8453 (mmmm) REVERT: C 33 TYR cc_start: 0.8305 (p90) cc_final: 0.8104 (p90) REVERT: C 34 TYR cc_start: 0.8378 (m-10) cc_final: 0.8061 (m-10) REVERT: C 36 ASP cc_start: 0.8501 (m-30) cc_final: 0.8202 (t0) REVERT: C 37 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 74 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8516 (mtmm) REVERT: C 91 TYR cc_start: 0.8953 (t80) cc_final: 0.8496 (t80) REVERT: C 93 TYR cc_start: 0.8719 (t80) cc_final: 0.8405 (t80) REVERT: H 4 LEU cc_start: 0.8848 (mm) cc_final: 0.8420 (mm) REVERT: H 31 ASP cc_start: 0.6772 (t0) cc_final: 0.6487 (t0) REVERT: H 38 MET cc_start: 0.8499 (ttt) cc_final: 0.7227 (ttm) REVERT: H 46 GLU cc_start: 0.8619 (pt0) cc_final: 0.8344 (pm20) REVERT: H 54 TYR cc_start: 0.8620 (t80) cc_final: 0.8393 (t80) REVERT: H 81 MET cc_start: 0.8213 (ttt) cc_final: 0.7899 (ttp) REVERT: H 106 MET cc_start: 0.8261 (mmm) cc_final: 0.7136 (mmt) REVERT: H 107 ASP cc_start: 0.7906 (t0) cc_final: 0.7402 (t0) REVERT: H 108 TYR cc_start: 0.8766 (m-80) cc_final: 0.8099 (m-80) REVERT: A 36 ASP cc_start: 0.8143 (m-30) cc_final: 0.7868 (t0) REVERT: A 41 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6992 (mt-10) REVERT: A 75 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7960 (tp40) REVERT: A 84 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 91 TYR cc_start: 0.9062 (t80) cc_final: 0.8819 (t80) REVERT: B 56 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8035 (ttpp) REVERT: B 75 GLN cc_start: 0.8066 (tp40) cc_final: 0.7751 (mm110) REVERT: B 83 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8311 (tptp) REVERT: B 87 ASP cc_start: 0.8833 (m-30) cc_final: 0.8309 (m-30) REVERT: B 117 PHE cc_start: 0.7980 (m-10) cc_final: 0.7746 (m-10) REVERT: D 84 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: E 24 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: E 28 ASP cc_start: 0.8082 (m-30) cc_final: 0.7727 (m-30) REVERT: E 41 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7703 (mt-10) REVERT: E 56 LYS cc_start: 0.8683 (tttt) cc_final: 0.8311 (ttpt) REVERT: E 83 LYS cc_start: 0.9071 (tptp) cc_final: 0.8743 (tppt) REVERT: E 87 ASP cc_start: 0.8711 (m-30) cc_final: 0.8358 (m-30) REVERT: E 88 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: E 93 TYR cc_start: 0.8291 (t80) cc_final: 0.7834 (t80) REVERT: E 110 TYR cc_start: 0.8131 (t80) cc_final: 0.7709 (t80) REVERT: G 85 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.7679 (mmm-85) REVERT: G 123 TYR cc_start: 0.8387 (m-10) cc_final: 0.8082 (m-10) REVERT: F 26 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: F 91 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.7586 (p0) REVERT: F 93 TYR cc_start: 0.8637 (m-80) cc_final: 0.8355 (m-80) REVERT: F 185 MET cc_start: 0.8985 (mpp) cc_final: 0.8477 (mpp) REVERT: F 210 GLU cc_start: 0.7171 (pm20) cc_final: 0.6357 (pm20) REVERT: F 213 GLU cc_start: 0.8142 (tp30) cc_final: 0.7340 (tp30) REVERT: F 223 GLU cc_start: 0.8104 (pt0) cc_final: 0.7576 (pt0) REVERT: F 248 GLU cc_start: 0.7149 (pm20) cc_final: 0.6854 (mp0) REVERT: F 260 TYR cc_start: 0.8754 (m-10) cc_final: 0.8389 (m-10) outliers start: 29 outliers final: 21 residues processed: 288 average time/residue: 0.2211 time to fit residues: 90.2696 Evaluate side-chains 285 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS H 5 GLN A 132 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.090987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077472 restraints weight = 24007.402| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.44 r_work: 0.3363 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10073 Z= 0.174 Angle : 0.689 10.853 13730 Z= 0.353 Chirality : 0.048 0.230 1521 Planarity : 0.005 0.060 1756 Dihedral : 4.517 22.473 1378 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.19 % Allowed : 24.30 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1247 helix: 0.11 (0.35), residues: 230 sheet: -0.89 (0.24), residues: 409 loop : -0.99 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 36 HIS 0.011 0.001 HIS K 28 PHE 0.024 0.002 PHE D 92 TYR 0.016 0.001 TYR A 93 ARG 0.011 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 330) hydrogen bonds : angle 5.76663 ( 906) SS BOND : bond 0.00263 ( 14) SS BOND : angle 0.83539 ( 28) covalent geometry : bond 0.00402 (10059) covalent geometry : angle 0.68916 (13702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8687 (t) cc_final: 0.7420 (t) REVERT: K 54 LEU cc_start: 0.8786 (tp) cc_final: 0.8577 (tp) REVERT: K 69 LYS cc_start: 0.8905 (mtpp) cc_final: 0.8489 (mmmm) REVERT: C 33 TYR cc_start: 0.8397 (p90) cc_final: 0.8124 (p90) REVERT: C 36 ASP cc_start: 0.8521 (m-30) cc_final: 0.8225 (t0) REVERT: C 37 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8047 (mm-30) REVERT: C 74 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8550 (mtmm) REVERT: C 82 PHE cc_start: 0.8443 (t80) cc_final: 0.7999 (t80) REVERT: C 91 TYR cc_start: 0.9008 (t80) cc_final: 0.8510 (t80) REVERT: H 4 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8379 (mm) REVERT: H 31 ASP cc_start: 0.6860 (t0) cc_final: 0.6622 (t0) REVERT: H 36 TRP cc_start: 0.8697 (m100) cc_final: 0.7702 (m100) REVERT: H 38 MET cc_start: 0.8448 (ttt) cc_final: 0.7276 (ttt) REVERT: H 46 GLU cc_start: 0.8605 (pt0) cc_final: 0.8321 (pm20) REVERT: H 54 TYR cc_start: 0.8660 (t80) cc_final: 0.8400 (t80) REVERT: H 81 MET cc_start: 0.8155 (ttt) cc_final: 0.7857 (ttp) REVERT: H 107 ASP cc_start: 0.8010 (t0) cc_final: 0.7470 (t0) REVERT: H 108 TYR cc_start: 0.8811 (m-80) cc_final: 0.8097 (m-80) REVERT: A 36 ASP cc_start: 0.8145 (m-30) cc_final: 0.7833 (t0) REVERT: A 41 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7027 (mt-10) REVERT: A 87 ASP cc_start: 0.8480 (m-30) cc_final: 0.8206 (m-30) REVERT: A 91 TYR cc_start: 0.9028 (t80) cc_final: 0.8741 (t80) REVERT: A 137 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7734 (mttp) REVERT: B 56 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8109 (ttpp) REVERT: B 75 GLN cc_start: 0.8227 (tp40) cc_final: 0.7910 (mm110) REVERT: B 83 LYS cc_start: 0.8956 (tmtt) cc_final: 0.8267 (tptp) REVERT: B 87 ASP cc_start: 0.8860 (m-30) cc_final: 0.8361 (m-30) REVERT: B 117 PHE cc_start: 0.7993 (m-10) cc_final: 0.7752 (m-10) REVERT: D 84 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: D 88 GLN cc_start: 0.8834 (tp40) cc_final: 0.8489 (tm-30) REVERT: E 28 ASP cc_start: 0.8042 (m-30) cc_final: 0.7680 (m-30) REVERT: E 41 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7958 (mt-10) REVERT: E 56 LYS cc_start: 0.8670 (tttt) cc_final: 0.8398 (ttmt) REVERT: E 83 LYS cc_start: 0.9070 (tptp) cc_final: 0.8690 (tppt) REVERT: E 87 ASP cc_start: 0.8729 (m-30) cc_final: 0.8440 (m-30) REVERT: E 88 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: E 93 TYR cc_start: 0.8345 (t80) cc_final: 0.7955 (t80) REVERT: E 110 TYR cc_start: 0.8126 (t80) cc_final: 0.7698 (t80) REVERT: G 85 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.7698 (mmm-85) REVERT: G 202 PRO cc_start: 0.9239 (Cg_exo) cc_final: 0.8961 (Cg_endo) REVERT: F 26 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: F 91 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.7607 (p0) REVERT: F 93 TYR cc_start: 0.8699 (m-80) cc_final: 0.8356 (m-80) REVERT: F 185 MET cc_start: 0.9041 (mpp) cc_final: 0.8536 (mpp) REVERT: F 210 GLU cc_start: 0.6794 (pm20) cc_final: 0.5896 (pm20) REVERT: F 213 GLU cc_start: 0.8206 (tp30) cc_final: 0.7436 (tp30) REVERT: F 223 GLU cc_start: 0.8083 (pt0) cc_final: 0.7525 (pt0) REVERT: F 248 GLU cc_start: 0.7169 (pm20) cc_final: 0.6803 (mp0) REVERT: F 260 TYR cc_start: 0.8791 (m-10) cc_final: 0.8451 (m-10) outliers start: 34 outliers final: 24 residues processed: 286 average time/residue: 0.2100 time to fit residues: 84.9924 Evaluate side-chains 288 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 30 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN ** F 160 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 = 0.3721 r_free = 0.3721 target = 0.089124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.075481 restraints weight = 24145.769| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.47 r_work: 0.3324 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.7810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10073 Z= 0.203 Angle : 0.699 10.823 13730 Z= 0.360 Chirality : 0.049 0.221 1521 Planarity : 0.005 0.055 1756 Dihedral : 4.635 24.099 1378 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.19 % Allowed : 24.77 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1247 helix: 0.01 (0.35), residues: 231 sheet: -0.91 (0.24), residues: 413 loop : -0.95 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 78 HIS 0.011 0.001 HIS K 28 PHE 0.025 0.002 PHE A 53 TYR 0.016 0.001 TYR A 93 ARG 0.011 0.001 ARG H 50 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 330) hydrogen bonds : angle 5.84176 ( 906) SS BOND : bond 0.00293 ( 14) SS BOND : angle 0.81850 ( 28) covalent geometry : bond 0.00464 (10059) covalent geometry : angle 0.69902 (13702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4667.45 seconds wall clock time: 82 minutes 18.07 seconds (4938.07 seconds total)