Starting phenix.real_space_refine on Fri Feb 14 03:46:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vx4_21429/02_2025/6vx4_21429.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx4_21429/02_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_21429/02_2025/6vx4_21429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx4_21429/02_2025/6vx4_21429.map" model { file = "/net/cci-nas-00/data/ceres_data/6vx4_21429/02_2025/6vx4_21429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx4_21429/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.74, per 1000 atoms: 0.58 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: 2.67 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: 1.45 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: 2.82 Time building geometry restraints manager: 3.09 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: 0.490 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.100 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- 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 10059 Z= 0.138 Angle : 0.433 5.845 13702 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 *********************** 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 : 1.084 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: 0.2364 time to fit residues: 136.8079 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 : 1.310 ------------------------------------------------------------------------------- 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 = 0.091251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077959 restraints weight = 23429.088| |-----------------------------------------------------------------------------| r_work (start): 0.3498 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 10059 Z= 0.422 Angle : 0.743 7.245 13702 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 *********************** 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 : 1.110 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: 0.7055 (t0) cc_final: 0.6762 (t0) REVERT: H 38 MET cc_start: 0.7578 (tmm) cc_final: 0.7218 (ttt) REVERT: H 108 TYR cc_start: 0.8933 (m-80) cc_final: 0.8514 (m-80) REVERT: A 33 TYR cc_start: 0.8897 (p90) cc_final: 0.8592 (p90) REVERT: A 36 ASP cc_start: 0.8013 (m-30) cc_final: 0.7339 (t0) REVERT: A 83 LYS cc_start: 0.9009 (pttt) cc_final: 0.8731 (tptt) REVERT: A 91 TYR cc_start: 0.8848 (t80) cc_final: 0.8506 (t80) REVERT: B 36 ASP cc_start: 0.7430 (t70) cc_final: 0.6923 (t0) REVERT: B 56 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7832 (ttpp) REVERT: B 59 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8164 (mmmt) REVERT: B 75 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7900 (mm110) REVERT: B 83 LYS cc_start: 0.8993 (tmtt) cc_final: 0.8046 (tptp) REVERT: B 87 ASP cc_start: 0.8687 (m-30) cc_final: 0.8353 (m-30) REVERT: B 109 THR cc_start: 0.8614 (m) cc_final: 0.8412 (p) REVERT: D 36 ASP cc_start: 0.8236 (t0) cc_final: 0.7984 (t0) REVERT: D 91 TYR cc_start: 0.8788 (t80) cc_final: 0.8579 (t80) REVERT: E 36 ASP cc_start: 0.7248 (t70) cc_final: 0.6897 (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: 0.8236 (t80) cc_final: 0.7972 (t80) REVERT: G 112 TYR cc_start: 0.8813 (t80) cc_final: 0.8345 (t80) REVERT: G 116 GLN cc_start: 0.7779 (tt0) cc_final: 0.6975 (tt0) REVERT: G 123 TYR cc_start: 0.8219 (m-80) cc_final: 0.7422 (m-10) REVERT: G 233 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7882 (mtm110) REVERT: G 237 GLU cc_start: 0.7780 (tp30) cc_final: 0.7343 (tp30) REVERT: F 26 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7082 (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: 0.2273 time to fit residues: 110.1277 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 : 1.123 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.091652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078552 restraints weight = 23716.152| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.27 r_work: 0.3382 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10059 Z= 0.269 Angle : 0.633 7.493 13702 Z= 0.333 Chirality : 0.048 0.194 1521 Planarity : 0.005 0.055 1756 Dihedral : 4.517 21.613 1378 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.00 % Allowed : 20.36 % Favored : 76.64 % 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: -0.47 (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 0.017 0.002 TRP F 32 HIS 0.009 0.001 HIS F 259 PHE 0.020 0.002 PHE F 156 TYR 0.026 0.002 TYR D 33 ARG 0.017 0.001 ARG F 118 *********************** 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 : 1.129 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 69 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8596 (mtmm) REVERT: K 92 TRP cc_start: 0.8669 (t-100) cc_final: 0.8433 (t-100) REVERT: C 36 ASP cc_start: 0.8526 (m-30) cc_final: 0.7993 (t0) REVERT: C 91 TYR cc_start: 0.8788 (t80) cc_final: 0.8386 (t80) REVERT: H 23 LYS cc_start: 0.9240 (tptp) cc_final: 0.8967 (tppp) REVERT: H 31 ASP cc_start: 0.6866 (t0) cc_final: 0.6610 (t0) REVERT: H 46 GLU cc_start: 0.8679 (pt0) cc_final: 0.8124 (pt0) REVERT: H 54 TYR cc_start: 0.8500 (t80) cc_final: 0.8280 (t80) REVERT: H 82 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8217 (mm-30) REVERT: H 107 ASP cc_start: 0.8442 (t0) cc_final: 0.8122 (t0) REVERT: H 108 TYR cc_start: 0.9037 (m-80) cc_final: 0.8339 (m-80) REVERT: A 36 ASP cc_start: 0.8087 (m-30) cc_final: 0.7823 (t70) REVERT: A 41 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6556 (mt-10) REVERT: A 84 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 91 TYR cc_start: 0.8970 (t80) cc_final: 0.8663 (t80) REVERT: B 36 ASP cc_start: 0.7290 (t70) cc_final: 0.7011 (t0) REVERT: B 37 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 56 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7914 (tttm) REVERT: B 59 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8410 (mmmt) REVERT: B 75 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7805 (mm110) REVERT: B 83 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8036 (tptp) REVERT: B 87 ASP cc_start: 0.8697 (m-30) cc_final: 0.8255 (m-30) REVERT: D 36 ASP cc_start: 0.8212 (t0) cc_final: 0.7964 (t0) REVERT: D 83 LYS cc_start: 0.9081 (tppt) cc_final: 0.8871 (tppp) REVERT: D 91 TYR cc_start: 0.8716 (t80) cc_final: 0.8437 (t80) REVERT: E 28 ASP cc_start: 0.7654 (m-30) cc_final: 0.7338 (m-30) REVERT: E 36 ASP cc_start: 0.7126 (t70) cc_final: 0.6901 (t70) REVERT: E 41 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7951 (mt-10) REVERT: E 56 LYS cc_start: 0.8719 (tttt) cc_final: 0.8434 (ttmt) REVERT: E 83 LYS cc_start: 0.9090 (tptp) cc_final: 0.8537 (tppt) REVERT: E 84 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8250 (mm-30) REVERT: E 87 ASP cc_start: 0.8670 (m-30) cc_final: 0.8322 (m-30) REVERT: E 88 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: E 104 GLN cc_start: 0.7534 (tt0) cc_final: 0.7325 (tt0) REVERT: E 110 TYR cc_start: 0.7977 (t80) cc_final: 0.7744 (t80) REVERT: G 85 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.7781 (mmm-85) REVERT: G 112 TYR cc_start: 0.8714 (t80) cc_final: 0.8303 (t80) REVERT: G 123 TYR cc_start: 0.8195 (m-80) cc_final: 0.7455 (m-10) REVERT: G 233 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7924 (mtm110) REVERT: G 237 GLU cc_start: 0.7638 (tp30) cc_final: 0.7157 (tp30) REVERT: F 26 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: F 91 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.7926 (p0) REVERT: F 93 TYR cc_start: 0.8519 (m-80) cc_final: 0.8065 (m-80) REVERT: F 204 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7611 (mt-10) REVERT: F 208 MET cc_start: 0.7078 (mmm) cc_final: 0.6857 (mmm) REVERT: F 213 GLU cc_start: 0.8166 (tp30) cc_final: 0.7599 (tp30) outliers start: 32 outliers final: 21 residues processed: 324 average time/residue: 0.2306 time to fit residues: 102.6623 Evaluate side-chains 297 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE 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: 0.9980 chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 15 GLN K 28 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.087602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074384 restraints weight = 23904.227| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.26 r_work: 0.3298 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10059 Z= 0.345 Angle : 0.656 7.709 13702 Z= 0.341 Chirality : 0.048 0.204 1521 Planarity : 0.005 0.065 1756 Dihedral : 4.629 21.422 1378 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.50 % Allowed : 19.98 % Favored : 75.52 % 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: -1.86 (0.23), residues: 1247 helix: -0.19 (0.36), residues: 212 sheet: -1.55 (0.23), residues: 410 loop : -1.29 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 78 HIS 0.011 0.002 HIS F 259 PHE 0.022 0.002 PHE F 156 TYR 0.015 0.002 TYR G 95 ARG 0.014 0.001 ARG F 118 *********************** 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 331 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 69 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8705 (mtmm) REVERT: K 92 TRP cc_start: 0.8689 (t-100) cc_final: 0.8216 (t-100) REVERT: C 36 ASP cc_start: 0.8703 (m-30) cc_final: 0.8181 (t0) REVERT: C 84 GLU cc_start: 0.7753 (mp0) cc_final: 0.7408 (mp0) REVERT: H 23 LYS cc_start: 0.9291 (tptp) cc_final: 0.9072 (tppp) REVERT: H 31 ASP cc_start: 0.7015 (t0) cc_final: 0.6743 (t0) REVERT: H 36 TRP cc_start: 0.8882 (m100) cc_final: 0.8563 (m100) REVERT: H 38 MET cc_start: 0.8386 (ttt) cc_final: 0.7399 (ttt) REVERT: H 46 GLU cc_start: 0.8699 (pt0) cc_final: 0.8243 (pm20) REVERT: H 54 TYR cc_start: 0.8575 (t80) cc_final: 0.8326 (t80) REVERT: H 69 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8557 (p) REVERT: H 81 MET cc_start: 0.8748 (ttt) cc_final: 0.8260 (ttp) REVERT: H 107 ASP cc_start: 0.8337 (t0) cc_final: 0.7989 (t0) REVERT: H 108 TYR cc_start: 0.8914 (m-80) cc_final: 0.8090 (m-80) REVERT: A 41 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6804 (mt-10) REVERT: A 91 TYR cc_start: 0.8953 (t80) cc_final: 0.8670 (t80) REVERT: B 28 ASP cc_start: 0.7990 (m-30) cc_final: 0.7474 (m-30) REVERT: B 36 ASP cc_start: 0.7682 (t70) cc_final: 0.7384 (t0) REVERT: B 56 LYS cc_start: 0.8496 (ttmt) cc_final: 0.7873 (tttm) REVERT: B 75 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7708 (mm110) REVERT: B 83 LYS cc_start: 0.8959 (tmtt) cc_final: 0.7999 (tptp) REVERT: B 87 ASP cc_start: 0.8823 (m-30) cc_final: 0.8314 (m-30) REVERT: D 36 ASP cc_start: 0.8387 (t0) cc_final: 0.8166 (t0) REVERT: D 41 GLU cc_start: 0.8828 (mp0) cc_final: 0.8360 (mm-30) REVERT: D 91 TYR cc_start: 0.8854 (t80) cc_final: 0.8568 (t80) REVERT: E 28 ASP cc_start: 0.7928 (m-30) cc_final: 0.7452 (m-30) REVERT: E 41 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7610 (mt-10) REVERT: E 56 LYS cc_start: 0.8662 (tttt) cc_final: 0.8256 (ttpt) REVERT: E 83 LYS cc_start: 0.9100 (tptp) cc_final: 0.8722 (tppt) REVERT: E 88 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: E 110 TYR cc_start: 0.8039 (t80) cc_final: 0.7693 (t80) REVERT: G 123 TYR cc_start: 0.8325 (m-80) cc_final: 0.7376 (m-10) REVERT: G 237 GLU cc_start: 0.7756 (tp30) cc_final: 0.7181 (tp30) REVERT: F 26 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: F 91 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.7958 (p0) REVERT: F 93 TYR cc_start: 0.8671 (m-80) cc_final: 0.8441 (m-80) REVERT: F 157 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9118 (mt) REVERT: F 185 MET cc_start: 0.9047 (mpp) cc_final: 0.8603 (mpp) REVERT: F 204 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7646 (mt-10) REVERT: F 208 MET cc_start: 0.7356 (mmm) cc_final: 0.6899 (mmm) REVERT: F 213 GLU cc_start: 0.8235 (tp30) cc_final: 0.7639 (tp30) REVERT: F 260 TYR cc_start: 0.8868 (m-80) cc_final: 0.8650 (m-10) outliers start: 48 outliers final: 27 residues processed: 313 average time/residue: 0.2277 time to fit residues: 98.5399 Evaluate side-chains 297 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 15 GLN 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.089297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076088 restraints weight = 23654.122| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.28 r_work: 0.3333 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10059 Z= 0.252 Angle : 0.619 8.664 13702 Z= 0.320 Chirality : 0.048 0.210 1521 Planarity : 0.004 0.048 1756 Dihedral : 4.496 20.147 1378 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.32 % Allowed : 20.73 % Favored : 74.95 % 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: -1.60 (0.23), residues: 1247 helix: 0.04 (0.36), residues: 212 sheet: -1.30 (0.24), residues: 401 loop : -1.21 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 78 HIS 0.008 0.001 HIS K 28 PHE 0.017 0.002 PHE F 156 TYR 0.013 0.001 TYR E 33 ARG 0.012 0.001 ARG F 118 *********************** 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 337 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 1.124 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: 0.8138 (OUTLIER) cc_final: 0.7777 (tp) REVERT: K 69 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8644 (mtmm) REVERT: K 92 TRP cc_start: 0.8517 (t-100) cc_final: 0.8131 (t-100) REVERT: C 36 ASP cc_start: 0.8593 (m-30) cc_final: 0.8146 (t0) REVERT: C 49 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8327 (p) REVERT: C 74 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8502 (mtmm) REVERT: C 82 PHE cc_start: 0.8594 (t80) cc_final: 0.8078 (t80) REVERT: C 83 LYS cc_start: 0.8456 (tmmt) cc_final: 0.8063 (tmmt) REVERT: C 91 TYR cc_start: 0.8886 (t80) cc_final: 0.8452 (t80) REVERT: H 31 ASP cc_start: 0.6898 (t0) cc_final: 0.6617 (t0) REVERT: H 37 VAL cc_start: 0.9198 (t) cc_final: 0.8997 (t) REVERT: H 38 MET cc_start: 0.8437 (ttt) cc_final: 0.7351 (ttt) REVERT: H 46 GLU cc_start: 0.8702 (pt0) cc_final: 0.8430 (pm20) REVERT: H 54 TYR cc_start: 0.8558 (t80) cc_final: 0.8327 (t80) REVERT: H 107 ASP cc_start: 0.8275 (t0) cc_final: 0.7896 (t0) REVERT: H 108 TYR cc_start: 0.8909 (m-80) cc_final: 0.8266 (m-80) REVERT: A 36 ASP cc_start: 0.8447 (m-30) cc_final: 0.7692 (t0) REVERT: A 41 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7078 (mt-10) REVERT: A 84 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 91 TYR cc_start: 0.9032 (t80) cc_final: 0.8772 (t80) REVERT: B 36 ASP cc_start: 0.7622 (t70) cc_final: 0.7253 (t0) REVERT: B 56 LYS cc_start: 0.8449 (ttmt) cc_final: 0.7825 (tttm) REVERT: B 75 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7768 (mm110) REVERT: B 83 LYS cc_start: 0.8885 (tmtt) cc_final: 0.7821 (tppt) REVERT: B 87 ASP cc_start: 0.8852 (m-30) cc_final: 0.8012 (m-30) REVERT: B 117 PHE cc_start: 0.8097 (m-10) cc_final: 0.7836 (m-10) REVERT: D 36 ASP cc_start: 0.8354 (t0) cc_final: 0.8144 (t0) REVERT: D 41 GLU cc_start: 0.8807 (mp0) cc_final: 0.8391 (mm-30) REVERT: D 88 GLN cc_start: 0.8735 (tp40) cc_final: 0.8482 (tp-100) REVERT: D 91 TYR cc_start: 0.8790 (t80) cc_final: 0.8513 (t80) REVERT: E 28 ASP cc_start: 0.7893 (m-30) cc_final: 0.7413 (m-30) REVERT: E 41 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 56 LYS cc_start: 0.8632 (tttt) cc_final: 0.8229 (ttpt) REVERT: E 83 LYS cc_start: 0.9084 (tptp) cc_final: 0.8760 (tppt) REVERT: E 87 ASP cc_start: 0.8680 (m-30) cc_final: 0.8407 (m-30) REVERT: E 88 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8718 (mm110) REVERT: E 104 GLN cc_start: 0.7312 (tt0) cc_final: 0.6947 (mt0) REVERT: E 110 TYR cc_start: 0.8071 (t80) cc_final: 0.7701 (t80) REVERT: G 85 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.7631 (mmm-85) REVERT: G 123 TYR cc_start: 0.8283 (m-80) cc_final: 0.7586 (m-10) REVERT: G 237 GLU cc_start: 0.7730 (tp30) cc_final: 0.7171 (tp30) REVERT: F 26 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: F 91 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.7696 (p0) REVERT: F 93 TYR cc_start: 0.8671 (m-80) cc_final: 0.8211 (m-80) REVERT: F 157 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9003 (mt) REVERT: F 185 MET cc_start: 0.9045 (mpp) cc_final: 0.8564 (mpp) REVERT: F 213 GLU cc_start: 0.8215 (tp30) cc_final: 0.7559 (tp30) outliers start: 46 outliers final: 30 residues processed: 320 average time/residue: 0.2070 time to fit residues: 93.7242 Evaluate side-chains 307 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 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 157 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: 9.9990 chunk 96 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.087979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074812 restraints weight = 23850.218| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.23 r_work: 0.3306 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10059 Z= 0.299 Angle : 0.643 11.207 13702 Z= 0.328 Chirality : 0.049 0.257 1521 Planarity : 0.005 0.049 1756 Dihedral : 4.516 20.396 1378 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.69 % Allowed : 22.51 % Favored : 72.80 % 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: -1.54 (0.23), residues: 1247 helix: -0.02 (0.36), residues: 218 sheet: -1.26 (0.24), residues: 412 loop : -1.12 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 78 HIS 0.009 0.001 HIS F 259 PHE 0.019 0.002 PHE F 156 TYR 0.016 0.001 TYR H 27 ARG 0.010 0.001 ARG F 118 *********************** 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 333 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8836 (t) cc_final: 0.7787 (t) REVERT: K 69 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8729 (mtmm) REVERT: C 36 ASP cc_start: 0.8582 (m-30) cc_final: 0.8118 (t0) REVERT: C 37 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 49 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8358 (p) REVERT: C 74 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8549 (mtmm) REVERT: C 91 TYR cc_start: 0.8941 (t80) cc_final: 0.8499 (t80) REVERT: H 4 LEU cc_start: 0.8832 (mm) cc_final: 0.8183 (mm) REVERT: H 31 ASP cc_start: 0.6904 (t0) cc_final: 0.6633 (t0) REVERT: H 37 VAL cc_start: 0.9241 (t) cc_final: 0.8985 (t) REVERT: H 38 MET cc_start: 0.8594 (ttt) cc_final: 0.7239 (ttm) REVERT: H 45 LEU cc_start: 0.9286 (mt) cc_final: 0.9001 (tp) REVERT: H 46 GLU cc_start: 0.8716 (pt0) cc_final: 0.8362 (pm20) REVERT: H 54 TYR cc_start: 0.8691 (t80) cc_final: 0.8439 (t80) REVERT: H 107 ASP cc_start: 0.8093 (t0) cc_final: 0.7638 (t0) REVERT: H 108 TYR cc_start: 0.8892 (m-80) cc_final: 0.8106 (m-80) REVERT: A 36 ASP cc_start: 0.8310 (m-30) cc_final: 0.7971 (t0) REVERT: A 41 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 84 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7661 (mm-30) REVERT: A 91 TYR cc_start: 0.9078 (t80) cc_final: 0.8818 (t80) REVERT: B 28 ASP cc_start: 0.7881 (m-30) cc_final: 0.7423 (m-30) REVERT: B 36 ASP cc_start: 0.7713 (t70) cc_final: 0.7440 (t0) REVERT: B 56 LYS cc_start: 0.8501 (ttmt) cc_final: 0.7868 (tttm) REVERT: B 75 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7849 (mm110) REVERT: B 83 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8018 (tppt) REVERT: B 87 ASP cc_start: 0.8839 (m-30) cc_final: 0.8012 (m-30) REVERT: B 120 ASN cc_start: 0.8023 (m-40) cc_final: 0.7814 (m-40) REVERT: D 41 GLU cc_start: 0.8825 (mp0) cc_final: 0.8420 (mm-30) REVERT: D 84 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: D 91 TYR cc_start: 0.8831 (t80) cc_final: 0.8498 (t80) REVERT: E 28 ASP cc_start: 0.7920 (m-30) cc_final: 0.7504 (m-30) REVERT: E 41 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7854 (mt-10) REVERT: E 56 LYS cc_start: 0.8719 (tttt) cc_final: 0.8343 (ttpt) REVERT: E 83 LYS cc_start: 0.9081 (tptp) cc_final: 0.8740 (tppt) REVERT: E 84 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 87 ASP cc_start: 0.8705 (m-30) cc_final: 0.8486 (m-30) REVERT: E 88 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8482 (mp10) REVERT: E 103 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8490 (p) REVERT: E 104 GLN cc_start: 0.7436 (tt0) cc_final: 0.6861 (mt0) REVERT: E 110 TYR cc_start: 0.8185 (t80) cc_final: 0.7802 (t80) REVERT: G 123 TYR cc_start: 0.8346 (m-80) cc_final: 0.7409 (m-10) REVERT: G 237 GLU cc_start: 0.7705 (tp30) cc_final: 0.7233 (tp30) REVERT: F 26 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: F 91 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.7809 (p0) REVERT: F 93 TYR cc_start: 0.8741 (m-80) cc_final: 0.8228 (m-80) REVERT: F 157 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9023 (mt) REVERT: F 185 MET cc_start: 0.9025 (mpp) cc_final: 0.8543 (mpp) REVERT: F 204 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7631 (mt-10) REVERT: F 213 GLU cc_start: 0.8259 (tp30) cc_final: 0.7496 (tp30) REVERT: F 260 TYR cc_start: 0.8935 (m-80) cc_final: 0.8705 (m-10) outliers start: 50 outliers final: 35 residues processed: 308 average time/residue: 0.2048 time to fit residues: 90.2756 Evaluate side-chains 315 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 49 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 57 ASP Chi-restraints excluded: chain H residue 71 THR 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 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 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 103 VAL 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 157 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: 4.9990 chunk 61 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.0370 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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 75 GLN D 88 GLN D 97 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.090073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076624 restraints weight = 23932.103| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.28 r_work: 0.3345 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.7248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 10059 Z= 0.248 Angle : 0.660 15.414 13702 Z= 0.336 Chirality : 0.049 0.317 1521 Planarity : 0.004 0.043 1756 Dihedral : 4.506 19.676 1378 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.85 % Allowed : 23.36 % Favored : 72.80 % 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: -1.39 (0.24), residues: 1247 helix: 0.07 (0.36), residues: 218 sheet: -1.11 (0.24), residues: 408 loop : -1.05 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 78 HIS 0.007 0.001 HIS F 259 PHE 0.017 0.002 PHE B 117 TYR 0.016 0.001 TYR C 34 ARG 0.008 0.001 ARG F 118 *********************** 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 334 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 1.217 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: 0.8823 (t) cc_final: 0.7756 (t) REVERT: K 54 LEU cc_start: 0.8861 (tp) cc_final: 0.8649 (tp) REVERT: K 69 LYS cc_start: 0.8876 (mtmm) cc_final: 0.8671 (mtmm) REVERT: C 33 TYR cc_start: 0.8394 (p90) cc_final: 0.8158 (p90) REVERT: C 36 ASP cc_start: 0.8553 (m-30) cc_final: 0.8144 (t0) REVERT: C 37 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8029 (mm-30) REVERT: C 74 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8549 (mtmm) REVERT: C 82 PHE cc_start: 0.8542 (t80) cc_final: 0.8119 (t80) REVERT: C 83 LYS cc_start: 0.8632 (tmmt) cc_final: 0.8286 (tmmt) REVERT: C 84 GLU cc_start: 0.7956 (mp0) cc_final: 0.7708 (mm-30) REVERT: C 91 TYR cc_start: 0.8930 (t80) cc_final: 0.8486 (t80) REVERT: H 4 LEU cc_start: 0.8793 (mm) cc_final: 0.8274 (mm) REVERT: H 31 ASP cc_start: 0.6841 (t0) cc_final: 0.6600 (t0) REVERT: H 38 MET cc_start: 0.8621 (ttt) cc_final: 0.7624 (ttt) REVERT: H 46 GLU cc_start: 0.8725 (pt0) cc_final: 0.8433 (pm20) REVERT: H 54 TYR cc_start: 0.8687 (t80) cc_final: 0.8415 (t80) REVERT: H 107 ASP cc_start: 0.8018 (t0) cc_final: 0.7519 (t0) REVERT: H 108 TYR cc_start: 0.8813 (m-80) cc_final: 0.8033 (m-80) REVERT: A 36 ASP cc_start: 0.8247 (m-30) cc_final: 0.7937 (t0) REVERT: A 41 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 91 TYR cc_start: 0.9046 (t80) cc_final: 0.8788 (t80) REVERT: B 28 ASP cc_start: 0.7922 (m-30) cc_final: 0.7633 (m-30) REVERT: B 36 ASP cc_start: 0.7696 (t70) cc_final: 0.7443 (t70) REVERT: B 56 LYS cc_start: 0.8509 (ttmt) cc_final: 0.7865 (tttm) REVERT: B 75 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7869 (mm110) REVERT: B 83 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8259 (tptp) REVERT: B 87 ASP cc_start: 0.8842 (m-30) cc_final: 0.8407 (m-30) REVERT: B 117 PHE cc_start: 0.8178 (m-10) cc_final: 0.7944 (m-10) REVERT: B 120 ASN cc_start: 0.7886 (m-40) cc_final: 0.7661 (m-40) REVERT: D 41 GLU cc_start: 0.8799 (mp0) cc_final: 0.8403 (mm-30) REVERT: D 84 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: D 91 TYR cc_start: 0.8801 (t80) cc_final: 0.7810 (t80) REVERT: E 28 ASP cc_start: 0.7929 (m-30) cc_final: 0.7530 (m-30) REVERT: E 41 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7965 (mt-10) REVERT: E 56 LYS cc_start: 0.8747 (tttt) cc_final: 0.8373 (ttpt) REVERT: E 75 GLN cc_start: 0.7919 (mm110) cc_final: 0.7673 (mp10) REVERT: E 83 LYS cc_start: 0.9094 (tptp) cc_final: 0.8764 (tppt) REVERT: E 87 ASP cc_start: 0.8668 (m-30) cc_final: 0.8413 (m-30) REVERT: E 93 TYR cc_start: 0.8756 (t80) cc_final: 0.8199 (t80) REVERT: E 103 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8462 (p) REVERT: E 104 GLN cc_start: 0.7453 (tt0) cc_final: 0.6839 (mt0) REVERT: E 110 TYR cc_start: 0.8147 (t80) cc_final: 0.7681 (t80) REVERT: G 85 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.7658 (mmm-85) REVERT: G 123 TYR cc_start: 0.8337 (m-80) cc_final: 0.7646 (m-10) REVERT: G 237 GLU cc_start: 0.7720 (tp30) cc_final: 0.7254 (tp30) REVERT: F 26 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: F 91 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.7788 (p0) REVERT: F 93 TYR cc_start: 0.8751 (m-80) cc_final: 0.8294 (m-80) REVERT: F 185 MET cc_start: 0.8979 (mpp) cc_final: 0.8504 (mpp) REVERT: F 213 GLU cc_start: 0.8235 (tp30) cc_final: 0.7470 (tp30) REVERT: F 260 TYR cc_start: 0.8921 (m-80) cc_final: 0.8700 (m-80) outliers start: 41 outliers final: 28 residues processed: 314 average time/residue: 0.2113 time to fit residues: 93.6365 Evaluate side-chains 305 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 57 ASP 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 A residue 123 VAL Chi-restraints excluded: chain B residue 75 GLN 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 58 VAL Chi-restraints excluded: chain E residue 103 VAL 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 238 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 109 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS D 31 ASN D 88 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.087186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.073810 restraints weight = 24092.022| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.27 r_work: 0.3287 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.7478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 10059 Z= 0.352 Angle : 0.711 14.537 13702 Z= 0.365 Chirality : 0.050 0.323 1521 Planarity : 0.005 0.071 1756 Dihedral : 4.658 21.241 1378 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.03 % Allowed : 23.83 % Favored : 72.14 % 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: -1.50 (0.24), residues: 1247 helix: -0.18 (0.35), residues: 223 sheet: -1.17 (0.24), residues: 414 loop : -1.07 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 78 HIS 0.008 0.001 HIS F 259 PHE 0.021 0.002 PHE F 156 TYR 0.019 0.002 TYR H 27 ARG 0.007 0.001 ARG H 50 *********************** 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 323 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 1.108 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: 0.8899 (t) cc_final: 0.7697 (t) REVERT: K 69 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8706 (mtmm) REVERT: C 33 TYR cc_start: 0.8571 (p90) cc_final: 0.8346 (p90) REVERT: C 36 ASP cc_start: 0.8557 (m-30) cc_final: 0.8151 (t0) REVERT: C 37 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8128 (mm-30) REVERT: C 74 LYS cc_start: 0.9055 (mtmm) cc_final: 0.8623 (mtmm) REVERT: H 4 LEU cc_start: 0.8753 (mm) cc_final: 0.8438 (mm) REVERT: H 36 TRP cc_start: 0.8718 (m100) cc_final: 0.7944 (m100) REVERT: H 38 MET cc_start: 0.8707 (ttt) cc_final: 0.7301 (ttm) REVERT: H 46 GLU cc_start: 0.8656 (pt0) cc_final: 0.8378 (pm20) REVERT: H 54 TYR cc_start: 0.8716 (t80) cc_final: 0.8372 (t80) REVERT: H 81 MET cc_start: 0.8636 (ttt) cc_final: 0.8261 (ttp) REVERT: H 107 ASP cc_start: 0.7889 (t0) cc_final: 0.7314 (t0) REVERT: H 108 TYR cc_start: 0.8744 (m-80) cc_final: 0.7838 (m-80) REVERT: A 33 TYR cc_start: 0.8220 (p90) cc_final: 0.7967 (p90) REVERT: A 36 ASP cc_start: 0.8290 (m-30) cc_final: 0.7952 (t0) REVERT: A 41 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7230 (mt-10) REVERT: A 91 TYR cc_start: 0.9068 (t80) cc_final: 0.8821 (t80) REVERT: B 28 ASP cc_start: 0.7998 (m-30) cc_final: 0.7699 (m-30) REVERT: B 56 LYS cc_start: 0.8612 (ttmt) cc_final: 0.7975 (tttm) REVERT: B 75 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8031 (mm110) REVERT: B 83 LYS cc_start: 0.9007 (tmtt) cc_final: 0.8107 (tptp) REVERT: B 84 GLU cc_start: 0.8250 (mp0) cc_final: 0.8025 (mp0) REVERT: B 87 ASP cc_start: 0.8923 (m-30) cc_final: 0.8401 (m-30) REVERT: B 117 PHE cc_start: 0.8241 (m-10) cc_final: 0.8009 (m-10) REVERT: D 41 GLU cc_start: 0.8817 (mp0) cc_final: 0.8441 (mm-30) REVERT: D 84 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: D 91 TYR cc_start: 0.8859 (t80) cc_final: 0.8602 (t80) REVERT: E 28 ASP cc_start: 0.8046 (m-30) cc_final: 0.7673 (m-30) REVERT: E 41 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7980 (mt-10) REVERT: E 56 LYS cc_start: 0.8792 (tttt) cc_final: 0.8434 (ttpt) REVERT: E 83 LYS cc_start: 0.9091 (tptp) cc_final: 0.8731 (tppt) REVERT: E 87 ASP cc_start: 0.8724 (m-30) cc_final: 0.8419 (m-30) REVERT: E 88 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8747 (mm110) REVERT: E 110 TYR cc_start: 0.8202 (t80) cc_final: 0.7739 (t80) REVERT: G 85 ARG cc_start: 0.8630 (mmm-85) cc_final: 0.7666 (mmm-85) REVERT: G 123 TYR cc_start: 0.8438 (m-80) cc_final: 0.7563 (m-10) REVERT: G 237 GLU cc_start: 0.7776 (tp30) cc_final: 0.7283 (tp30) REVERT: F 26 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: F 91 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.7634 (p0) REVERT: F 93 TYR cc_start: 0.8818 (m-80) cc_final: 0.8262 (m-80) REVERT: F 185 MET cc_start: 0.9069 (mpp) cc_final: 0.8615 (mpp) REVERT: F 204 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7748 (mt-10) REVERT: F 208 MET cc_start: 0.6956 (mmm) cc_final: 0.6477 (mmm) REVERT: F 213 GLU cc_start: 0.8296 (tp30) cc_final: 0.7426 (tp30) REVERT: F 248 GLU cc_start: 0.7239 (pm20) cc_final: 0.6905 (mp0) outliers start: 43 outliers final: 30 residues processed: 302 average time/residue: 0.2111 time to fit residues: 90.8893 Evaluate side-chains 307 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 57 ASP 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 A residue 123 VAL Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL 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 63 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 B 120 ASN D 88 GLN D 97 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 121 ASN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.087546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074230 restraints weight = 23979.045| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.27 r_work: 0.3296 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10059 Z= 0.311 Angle : 0.691 14.362 13702 Z= 0.355 Chirality : 0.050 0.281 1521 Planarity : 0.005 0.060 1756 Dihedral : 4.656 20.558 1378 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.85 % Allowed : 23.36 % Favored : 72.80 % 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: -1.41 (0.24), residues: 1247 helix: -0.06 (0.36), residues: 218 sheet: -1.12 (0.24), residues: 416 loop : -1.01 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 78 HIS 0.009 0.001 HIS K 28 PHE 0.020 0.002 PHE F 156 TYR 0.019 0.002 TYR C 91 ARG 0.005 0.001 ARG F 251 *********************** 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 317 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 1.000 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: 0.8934 (t) cc_final: 0.8405 (t) REVERT: K 69 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8681 (mtmm) REVERT: C 33 TYR cc_start: 0.8568 (p90) cc_final: 0.8205 (p90) REVERT: C 36 ASP cc_start: 0.8556 (m-30) cc_final: 0.8184 (t0) REVERT: C 37 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8151 (mm-30) REVERT: C 41 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7648 (mm-30) REVERT: C 74 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8592 (mtmm) REVERT: C 91 TYR cc_start: 0.8997 (t80) cc_final: 0.8612 (t80) REVERT: H 4 LEU cc_start: 0.8758 (mm) cc_final: 0.8383 (mm) REVERT: H 38 MET cc_start: 0.8629 (ttt) cc_final: 0.7649 (ttt) REVERT: H 46 GLU cc_start: 0.8722 (pt0) cc_final: 0.8453 (pm20) REVERT: H 52 ASP cc_start: 0.8170 (t0) cc_final: 0.7797 (t0) REVERT: H 54 TYR cc_start: 0.8736 (t80) cc_final: 0.8355 (t80) REVERT: H 57 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7951 (p0) REVERT: H 81 MET cc_start: 0.8585 (ttt) cc_final: 0.8205 (ttp) REVERT: H 107 ASP cc_start: 0.7829 (t0) cc_final: 0.7243 (t0) REVERT: H 108 TYR cc_start: 0.8756 (m-80) cc_final: 0.7943 (m-80) REVERT: A 36 ASP cc_start: 0.8216 (m-30) cc_final: 0.7881 (t0) REVERT: A 41 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 86 LEU cc_start: 0.9236 (tp) cc_final: 0.8983 (tp) REVERT: A 112 LEU cc_start: 0.8934 (mt) cc_final: 0.8465 (mp) REVERT: A 115 ASN cc_start: 0.8864 (m-40) cc_final: 0.8370 (p0) REVERT: B 28 ASP cc_start: 0.7945 (m-30) cc_final: 0.7651 (m-30) REVERT: B 56 LYS cc_start: 0.8611 (ttmt) cc_final: 0.7961 (tttm) REVERT: B 59 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8479 (mmmt) REVERT: B 75 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8012 (mm110) REVERT: B 83 LYS cc_start: 0.8997 (tmtt) cc_final: 0.8199 (tptp) REVERT: B 87 ASP cc_start: 0.8874 (m-30) cc_final: 0.8454 (m-30) REVERT: B 117 PHE cc_start: 0.8270 (m-10) cc_final: 0.8042 (m-10) REVERT: D 26 THR cc_start: 0.8705 (t) cc_final: 0.8501 (m) REVERT: D 41 GLU cc_start: 0.8766 (mp0) cc_final: 0.8413 (mm-30) REVERT: D 84 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: D 91 TYR cc_start: 0.8846 (t80) cc_final: 0.7912 (t80) REVERT: E 28 ASP cc_start: 0.8000 (m-30) cc_final: 0.7645 (m-30) REVERT: E 41 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7965 (mt-10) REVERT: E 56 LYS cc_start: 0.8789 (tttt) cc_final: 0.8427 (ttpt) REVERT: E 75 GLN cc_start: 0.8003 (mm110) cc_final: 0.7720 (mp10) REVERT: E 83 LYS cc_start: 0.9084 (tptp) cc_final: 0.8723 (tppt) REVERT: E 88 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: E 93 TYR cc_start: 0.8877 (t80) cc_final: 0.8351 (t80) REVERT: E 110 TYR cc_start: 0.8159 (t80) cc_final: 0.7683 (t80) REVERT: G 85 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.7711 (mmm-85) REVERT: G 123 TYR cc_start: 0.8485 (m-80) cc_final: 0.7592 (m-10) REVERT: G 237 GLU cc_start: 0.7769 (tp30) cc_final: 0.7277 (tp30) REVERT: F 26 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: F 91 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.7667 (p0) REVERT: F 93 TYR cc_start: 0.8834 (m-80) cc_final: 0.8326 (m-80) REVERT: F 185 MET cc_start: 0.9039 (mpp) cc_final: 0.8543 (mpp) REVERT: F 204 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7721 (mt-10) REVERT: F 208 MET cc_start: 0.7058 (mmm) cc_final: 0.6519 (mmm) REVERT: F 210 GLU cc_start: 0.7520 (pm20) cc_final: 0.6708 (pm20) REVERT: F 223 GLU cc_start: 0.8238 (pt0) cc_final: 0.7711 (pt0) REVERT: F 248 GLU cc_start: 0.7283 (pm20) cc_final: 0.6816 (mp0) REVERT: F 260 TYR cc_start: 0.8849 (m-80) cc_final: 0.8485 (m-10) outliers start: 41 outliers final: 30 residues processed: 298 average time/residue: 0.2053 time to fit residues: 87.1303 Evaluate side-chains 301 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 H residue 57 ASP Chi-restraints excluded: chain H residue 71 THR 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 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 B residue 75 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 0.0870 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS A 132 GLN D 97 GLN ** E 104 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.089970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076274 restraints weight = 24148.077| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.42 r_work: 0.3358 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.7816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10059 Z= 0.240 Angle : 0.685 14.520 13702 Z= 0.350 Chirality : 0.049 0.260 1521 Planarity : 0.005 0.058 1756 Dihedral : 4.625 23.666 1378 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.00 % Allowed : 24.86 % Favored : 72.14 % 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: -1.39 (0.24), residues: 1247 helix: -0.12 (0.35), residues: 216 sheet: -1.09 (0.24), residues: 413 loop : -0.99 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 78 HIS 0.008 0.001 HIS K 28 PHE 0.017 0.002 PHE D 113 TYR 0.017 0.001 TYR C 91 ARG 0.007 0.001 ARG C 90 ********************** 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 310 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.189 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 49 SER cc_start: 0.8786 (t) cc_final: 0.7349 (t) REVERT: K 92 TRP cc_start: 0.8569 (t-100) cc_final: 0.8348 (t-100) REVERT: C 33 TYR cc_start: 0.8469 (p90) cc_final: 0.8207 (p90) REVERT: C 34 TYR cc_start: 0.8278 (m-10) cc_final: 0.7942 (m-10) REVERT: C 36 ASP cc_start: 0.8495 (m-30) cc_final: 0.8140 (t0) REVERT: C 37 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8114 (mm-30) REVERT: C 41 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7580 (mm-30) REVERT: C 91 TYR cc_start: 0.8931 (t80) cc_final: 0.8435 (t80) REVERT: H 4 LEU cc_start: 0.8683 (mm) cc_final: 0.8183 (mm) REVERT: H 32 TYR cc_start: 0.8116 (m-80) cc_final: 0.7637 (m-80) REVERT: H 36 TRP cc_start: 0.8790 (m100) cc_final: 0.7880 (m100) REVERT: H 38 MET cc_start: 0.8746 (ttt) cc_final: 0.7695 (ttt) REVERT: H 46 GLU cc_start: 0.8712 (pt0) cc_final: 0.8333 (pm20) REVERT: H 52 ASP cc_start: 0.8004 (t0) cc_final: 0.7544 (t0) REVERT: H 54 TYR cc_start: 0.8725 (t80) cc_final: 0.8358 (t80) REVERT: H 57 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8150 (p0) REVERT: H 81 MET cc_start: 0.8517 (ttt) cc_final: 0.7771 (ttp) REVERT: H 107 ASP cc_start: 0.7770 (t0) cc_final: 0.6807 (t70) REVERT: H 108 TYR cc_start: 0.8665 (m-80) cc_final: 0.7444 (m-80) REVERT: A 36 ASP cc_start: 0.8148 (m-30) cc_final: 0.7860 (t0) REVERT: A 41 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7196 (mt-10) REVERT: A 112 LEU cc_start: 0.8926 (mt) cc_final: 0.8438 (mp) REVERT: A 115 ASN cc_start: 0.8823 (m-40) cc_final: 0.8339 (p0) REVERT: B 56 LYS cc_start: 0.8451 (ttmt) cc_final: 0.7772 (tttm) REVERT: B 59 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8399 (mmmt) REVERT: B 75 GLN cc_start: 0.8311 (tp40) cc_final: 0.7989 (mm110) REVERT: B 83 LYS cc_start: 0.8996 (tmtt) cc_final: 0.8485 (tptp) REVERT: B 117 PHE cc_start: 0.8240 (m-10) cc_final: 0.7984 (m-10) REVERT: D 26 THR cc_start: 0.8651 (t) cc_final: 0.8411 (m) REVERT: D 41 GLU cc_start: 0.8606 (mp0) cc_final: 0.8260 (mm-30) REVERT: D 84 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: E 28 ASP cc_start: 0.8013 (m-30) cc_final: 0.7604 (m-30) REVERT: E 41 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7903 (mt-10) REVERT: E 56 LYS cc_start: 0.8772 (tttt) cc_final: 0.8398 (ttpt) REVERT: E 75 GLN cc_start: 0.7895 (mm110) cc_final: 0.7557 (mp10) REVERT: E 83 LYS cc_start: 0.9118 (tptp) cc_final: 0.8770 (tppt) REVERT: E 87 ASP cc_start: 0.8742 (m-30) cc_final: 0.8469 (m-30) REVERT: E 91 TYR cc_start: 0.8262 (t80) cc_final: 0.7932 (t80) REVERT: E 110 TYR cc_start: 0.8137 (t80) cc_final: 0.7633 (t80) REVERT: G 85 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.7783 (mmm-85) REVERT: F 26 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: F 42 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8252 (tp30) REVERT: F 66 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6635 (tm-30) REVERT: F 91 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.7588 (p0) REVERT: F 93 TYR cc_start: 0.8775 (m-80) cc_final: 0.8357 (m-80) REVERT: F 185 MET cc_start: 0.9047 (mpp) cc_final: 0.8542 (mpp) REVERT: F 195 ASP cc_start: 0.7490 (t0) cc_final: 0.7267 (t0) REVERT: F 204 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7733 (mt-10) REVERT: F 208 MET cc_start: 0.6981 (mmm) cc_final: 0.6409 (mmm) REVERT: F 210 GLU cc_start: 0.6992 (pm20) cc_final: 0.6380 (pm20) REVERT: F 213 GLU cc_start: 0.8176 (tp30) cc_final: 0.7378 (tp30) REVERT: F 223 GLU cc_start: 0.8242 (pt0) cc_final: 0.7698 (pt0) REVERT: F 248 GLU cc_start: 0.7288 (pm20) cc_final: 0.6836 (mp0) REVERT: F 260 TYR cc_start: 0.8671 (m-80) cc_final: 0.8269 (m-80) outliers start: 32 outliers final: 23 residues processed: 293 average time/residue: 0.2063 time to fit residues: 85.7702 Evaluate side-chains 292 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 HIS 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 H residue 57 ASP 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 D residue 38 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain E residue 58 VAL 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 124 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 232 LEU 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: 8.9990 chunk 83 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 61 ASN D 88 GLN D 97 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.086232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072500 restraints weight = 24323.225| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.38 r_work: 0.3266 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.7944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 10059 Z= 0.390 Angle : 0.738 14.567 13702 Z= 0.380 Chirality : 0.050 0.287 1521 Planarity : 0.005 0.057 1756 Dihedral : 4.853 26.214 1378 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.47 % Allowed : 24.77 % Favored : 71.76 % 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: -1.49 (0.24), residues: 1247 helix: -0.52 (0.36), residues: 211 sheet: -1.09 (0.24), residues: 408 loop : -0.96 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 78 HIS 0.006 0.001 HIS F 259 PHE 0.022 0.002 PHE F 156 TYR 0.023 0.002 TYR G 123 ARG 0.005 0.001 ARG C 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4571.12 seconds wall clock time: 82 minutes 22.03 seconds (4942.03 seconds total)