Starting phenix.real_space_refine on Wed Sep 17 16:28:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vx4_21429/09_2025/6vx4_21429.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vx4_21429/09_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_21429/09_2025/6vx4_21429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vx4_21429/09_2025/6vx4_21429.map" model { file = "/net/cci-nas-00/data/ceres_data/6vx4_21429/09_2025/6vx4_21429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vx4_21429/09_2025/6vx4_21429.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} 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: 2.39, per 1000 atoms: 0.24 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: 0.92 Conformation dependent library (CDL) restraints added in 356.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.39 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: 1.57 Time building geometry restraints manager: 1.20 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: 0.590 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10073 Z= 0.107 Angle : 0.433 5.845 13730 Z= 0.244 Chirality : 0.042 0.147 1521 Planarity : 0.002 0.050 1756 Dihedral : 12.959 89.090 3530 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG F 118 TYR 0.016 0.001 TYR G 95 PHE 0.005 0.001 PHE G 185 TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00211 (10059) covalent geometry : angle 0.43350 (13702) SS BOND : bond 0.00087 ( 14) SS BOND : angle 0.30336 ( 28) hydrogen bonds : bond 0.26272 ( 330) hydrogen bonds : angle 11.12039 ( 906) *********************** 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 : 0.370 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: H 31 ASP cc_start: 0.6372 (t0) cc_final: 0.6155 (t0) REVERT: H 52 ASP cc_start: 0.7112 (t0) cc_final: 0.6619 (t0) REVERT: H 61 ASN cc_start: 0.7136 (t0) cc_final: 0.6679 (t0) REVERT: H 94 TYR cc_start: 0.7921 (m-80) cc_final: 0.7641 (m-80) REVERT: H 108 TYR cc_start: 0.8311 (m-80) cc_final: 0.7997 (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: 0.6156 (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: 0.8110 (t80) REVERT: E 58 VAL cc_start: 0.8072 (m) cc_final: 0.7861 (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: 0.7223 (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: 0.0988 time to fit residues: 58.2467 Evaluate side-chains 299 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 296 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 GLN C 97 GLN C 132 GLN H 41 HIS A 61 ASN A 97 GLN B 115 ASN D 31 ASN D 88 GLN E 88 GLN E 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN G 102 ASN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.091851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078589 restraints weight = 23670.028| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.29 r_work: 0.3381 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10073 Z= 0.285 Angle : 0.725 7.193 13730 Z= 0.387 Chirality : 0.051 0.200 1521 Planarity : 0.007 0.156 1756 Dihedral : 4.926 21.619 1381 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.66 % Allowed : 17.54 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.22), residues: 1247 helix: -1.45 (0.31), residues: 221 sheet: -2.29 (0.22), residues: 420 loop : -1.94 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 118 TYR 0.020 0.002 TYR A 52 PHE 0.024 0.003 PHE F 156 TRP 0.016 0.002 TRP D 78 HIS 0.016 0.003 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00625 (10059) covalent geometry : angle 0.72499 (13702) SS BOND : bond 0.00463 ( 14) SS BOND : angle 0.80503 ( 28) hydrogen bonds : bond 0.04992 ( 330) hydrogen bonds : angle 7.05365 ( 906) *********************** 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 376 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 337 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 55 LYS cc_start: 0.8126 (tttm) cc_final: 0.7842 (ttpt) REVERT: K 92 TRP cc_start: 0.8842 (t-100) cc_final: 0.8531 (t-100) REVERT: H 23 LYS cc_start: 0.9223 (tptp) cc_final: 0.8810 (tptp) REVERT: H 31 ASP cc_start: 0.7049 (t0) cc_final: 0.6752 (t0) REVERT: H 38 MET cc_start: 0.7518 (tmm) cc_final: 0.6880 (ttt) REVERT: H 108 TYR cc_start: 0.8924 (m-80) cc_final: 0.8348 (m-80) REVERT: A 33 TYR cc_start: 0.8902 (p90) cc_final: 0.8580 (p90) REVERT: A 36 ASP cc_start: 0.7980 (m-30) cc_final: 0.7318 (t0) REVERT: A 83 LYS cc_start: 0.8994 (pttt) cc_final: 0.8731 (tptt) REVERT: A 91 TYR cc_start: 0.8801 (t80) cc_final: 0.8421 (t80) REVERT: B 56 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7630 (ttpt) REVERT: B 75 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7906 (mm110) REVERT: B 83 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8067 (tptp) REVERT: B 87 ASP cc_start: 0.8682 (m-30) cc_final: 0.8344 (m-30) REVERT: B 109 THR cc_start: 0.8602 (m) cc_final: 0.8392 (p) REVERT: B 112 LEU cc_start: 0.8666 (mm) cc_final: 0.8285 (mp) REVERT: B 115 ASN cc_start: 0.8605 (m-40) cc_final: 0.8306 (p0) REVERT: D 36 ASP cc_start: 0.8216 (t0) cc_final: 0.7949 (t0) REVERT: E 36 ASP cc_start: 0.7175 (t70) cc_final: 0.6834 (t0) REVERT: E 41 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8090 (mt-10) REVERT: E 56 LYS cc_start: 0.8710 (tttt) cc_final: 0.8389 (ttmt) REVERT: E 83 LYS cc_start: 0.9136 (tptp) cc_final: 0.8685 (tppt) REVERT: E 87 ASP cc_start: 0.8510 (m-30) cc_final: 0.8243 (m-30) REVERT: E 91 TYR cc_start: 0.8210 (t80) cc_final: 0.7899 (t80) REVERT: E 110 TYR cc_start: 0.8113 (t80) cc_final: 0.7897 (t80) REVERT: G 112 TYR cc_start: 0.8692 (t80) cc_final: 0.8227 (t80) REVERT: G 116 GLN cc_start: 0.7763 (tt0) cc_final: 0.6974 (tt0) REVERT: G 123 TYR cc_start: 0.8186 (m-80) cc_final: 0.7445 (m-10) REVERT: G 233 ARG cc_start: 0.8193 (mtm180) cc_final: 0.7036 (mtm-85) REVERT: G 237 GLU cc_start: 0.7763 (tp30) cc_final: 0.7360 (tp30) REVERT: F 27 TYR cc_start: 0.8625 (m-80) cc_final: 0.8364 (m-80) REVERT: F 91 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8108 (p0) REVERT: F 93 TYR cc_start: 0.8391 (m-80) cc_final: 0.8083 (m-80) REVERT: F 205 ASN cc_start: 0.8964 (t0) cc_final: 0.8574 (t0) REVERT: F 234 TYR cc_start: 0.8002 (p90) cc_final: 0.7794 (p90) outliers start: 39 outliers final: 23 residues processed: 352 average time/residue: 0.1073 time to fit residues: 52.8637 Evaluate side-chains 299 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 30 MET 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 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 93 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 110 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN B 104 GLN D 31 ASN D 88 GLN D 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN G 195 GLN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.094333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.081326 restraints weight = 23415.793| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.27 r_work: 0.3436 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10073 Z= 0.149 Angle : 0.631 8.658 13730 Z= 0.331 Chirality : 0.048 0.211 1521 Planarity : 0.005 0.061 1756 Dihedral : 4.469 20.947 1378 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.53 % Allowed : 21.20 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.23), residues: 1247 helix: -0.33 (0.36), residues: 211 sheet: -1.89 (0.23), residues: 412 loop : -1.48 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 118 TYR 0.015 0.001 TYR E 33 PHE 0.019 0.002 PHE D 113 TRP 0.016 0.002 TRP F 32 HIS 0.009 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00338 (10059) covalent geometry : angle 0.63108 (13702) SS BOND : bond 0.00437 ( 14) SS BOND : angle 0.64581 ( 28) hydrogen bonds : bond 0.03986 ( 330) hydrogen bonds : angle 6.17373 ( 906) *********************** 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 339 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 312 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 69 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8565 (mtmm) REVERT: K 82 ASP cc_start: 0.8378 (m-30) cc_final: 0.8119 (m-30) REVERT: K 92 TRP cc_start: 0.8420 (t-100) cc_final: 0.8203 (t-100) REVERT: C 34 TYR cc_start: 0.8159 (m-80) cc_final: 0.7872 (m-10) REVERT: C 36 ASP cc_start: 0.8394 (m-30) cc_final: 0.7831 (t0) REVERT: C 83 LYS cc_start: 0.8540 (tmtt) cc_final: 0.8289 (tmmt) REVERT: C 84 GLU cc_start: 0.7556 (mp0) cc_final: 0.7271 (mp0) REVERT: C 91 TYR cc_start: 0.8662 (t80) cc_final: 0.8318 (t80) REVERT: C 93 TYR cc_start: 0.7949 (t80) cc_final: 0.7549 (t80) REVERT: H 3 GLN cc_start: 0.7822 (pm20) cc_final: 0.7607 (pm20) REVERT: H 23 LYS cc_start: 0.9244 (tptp) cc_final: 0.8965 (tppp) REVERT: H 31 ASP cc_start: 0.6823 (t0) cc_final: 0.6507 (t0) REVERT: H 32 TYR cc_start: 0.8262 (m-80) cc_final: 0.7991 (m-80) REVERT: H 82 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8086 (mm-30) REVERT: H 107 ASP cc_start: 0.8436 (t0) cc_final: 0.7957 (t0) REVERT: H 108 TYR cc_start: 0.9000 (m-80) cc_final: 0.8301 (m-80) REVERT: A 36 ASP cc_start: 0.7980 (m-30) cc_final: 0.7731 (t70) REVERT: A 41 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6142 (mt-10) REVERT: A 91 TYR cc_start: 0.8850 (t80) cc_final: 0.8598 (t80) REVERT: A 115 ASN cc_start: 0.8496 (m-40) cc_final: 0.7867 (p0) REVERT: B 37 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8110 (mm-30) REVERT: B 56 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7883 (tttm) REVERT: B 75 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7760 (mm110) REVERT: B 83 LYS cc_start: 0.9026 (tmtt) cc_final: 0.7976 (tptp) REVERT: B 87 ASP cc_start: 0.8659 (m-30) cc_final: 0.8222 (m-30) REVERT: B 117 PHE cc_start: 0.7991 (m-10) cc_final: 0.7754 (m-10) REVERT: D 36 ASP cc_start: 0.8152 (t0) cc_final: 0.7725 (t0) REVERT: D 49 THR cc_start: 0.8920 (p) cc_final: 0.8710 (t) REVERT: D 83 LYS cc_start: 0.9075 (tppt) cc_final: 0.8830 (tppp) REVERT: D 88 GLN cc_start: 0.8369 (tp40) cc_final: 0.8053 (tp-100) REVERT: D 91 TYR cc_start: 0.8643 (t80) cc_final: 0.8254 (t80) REVERT: E 28 ASP cc_start: 0.7623 (m-30) cc_final: 0.7303 (m-30) REVERT: E 36 ASP cc_start: 0.6901 (t70) cc_final: 0.6459 (t0) REVERT: E 41 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7899 (mt-10) REVERT: E 56 LYS cc_start: 0.8631 (tttt) cc_final: 0.8386 (ttmt) REVERT: E 83 LYS cc_start: 0.9095 (tptp) cc_final: 0.8542 (tppt) REVERT: E 84 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8327 (mm-30) REVERT: E 87 ASP cc_start: 0.8590 (m-30) cc_final: 0.8214 (m-30) REVERT: E 88 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: E 110 TYR cc_start: 0.8177 (t80) cc_final: 0.7920 (t80) REVERT: E 115 ASN cc_start: 0.7811 (m110) cc_final: 0.7610 (m110) REVERT: G 85 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.7805 (mmm-85) REVERT: G 112 TYR cc_start: 0.8699 (t80) cc_final: 0.8309 (t80) REVERT: G 233 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7850 (mtm110) REVERT: F 26 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: F 27 TYR cc_start: 0.8639 (m-80) cc_final: 0.8271 (m-80) REVERT: F 91 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.7974 (p0) REVERT: F 93 TYR cc_start: 0.8307 (m-80) cc_final: 0.8086 (m-80) REVERT: F 204 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7649 (mt-10) REVERT: F 208 MET cc_start: 0.7178 (mmm) cc_final: 0.6911 (mmm) outliers start: 27 outliers final: 17 residues processed: 326 average time/residue: 0.1010 time to fit residues: 45.6598 Evaluate side-chains 299 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain H residue 75 SER 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 91 ASP Chi-restraints excluded: chain F residue 103 GLN 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 50 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS K 79 GLN H 5 GLN A 61 ASN D 97 GLN D 106 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** F 35 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070277 restraints weight = 24596.469| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.29 r_work: 0.3206 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10073 Z= 0.361 Angle : 0.757 9.229 13730 Z= 0.394 Chirality : 0.051 0.227 1521 Planarity : 0.006 0.092 1756 Dihedral : 5.070 21.654 1378 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.63 % Allowed : 18.57 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.23), residues: 1247 helix: -0.60 (0.33), residues: 229 sheet: -1.58 (0.23), residues: 392 loop : -1.62 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 61 TYR 0.019 0.002 TYR G 95 PHE 0.021 0.003 PHE F 156 TRP 0.023 0.002 TRP E 78 HIS 0.014 0.002 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00786 (10059) covalent geometry : angle 0.75662 (13702) SS BOND : bond 0.00501 ( 14) SS BOND : angle 0.84991 ( 28) hydrogen bonds : bond 0.05148 ( 330) hydrogen bonds : angle 6.51298 ( 906) *********************** 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 342 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8097 (tp) REVERT: C 36 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8032 (t0) REVERT: C 133 CYS cc_start: 0.6064 (m) cc_final: 0.5103 (m) REVERT: H 23 LYS cc_start: 0.9251 (tptp) cc_final: 0.9032 (tppp) REVERT: H 46 GLU cc_start: 0.8649 (pt0) cc_final: 0.8256 (tm-30) REVERT: H 61 ASN cc_start: 0.7510 (t0) cc_final: 0.7198 (t0) REVERT: H 107 ASP cc_start: 0.8426 (t0) cc_final: 0.8049 (t0) REVERT: H 108 TYR cc_start: 0.9005 (m-80) cc_final: 0.8450 (m-80) REVERT: A 33 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8256 (p90) REVERT: A 36 ASP cc_start: 0.8268 (m-30) cc_final: 0.7841 (t0) REVERT: A 41 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7479 (mt-10) REVERT: A 93 TYR cc_start: 0.8710 (t80) cc_final: 0.8387 (t80) REVERT: A 137 LYS cc_start: 0.7798 (ptpt) cc_final: 0.7585 (mttp) REVERT: B 28 ASP cc_start: 0.8085 (m-30) cc_final: 0.7557 (m-30) REVERT: B 56 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8070 (tttm) REVERT: B 75 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7862 (mm110) REVERT: B 83 LYS cc_start: 0.8932 (tmtt) cc_final: 0.7930 (tptp) REVERT: B 87 ASP cc_start: 0.8924 (m-30) cc_final: 0.8419 (m-30) REVERT: D 84 GLU cc_start: 0.8238 (mp0) cc_final: 0.7956 (mp0) REVERT: E 41 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8150 (mt-10) REVERT: E 56 LYS cc_start: 0.8773 (tttt) cc_final: 0.8445 (ttpt) REVERT: E 83 LYS cc_start: 0.9142 (tptp) cc_final: 0.8837 (tppt) REVERT: E 88 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (mm110) REVERT: E 110 TYR cc_start: 0.8212 (t80) cc_final: 0.7875 (t80) REVERT: E 115 ASN cc_start: 0.8080 (m110) cc_final: 0.7863 (m110) REVERT: G 123 TYR cc_start: 0.8350 (m-10) cc_final: 0.7435 (m-10) REVERT: G 233 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7979 (mtm110) REVERT: G 237 GLU cc_start: 0.8099 (tp30) cc_final: 0.7618 (tp30) REVERT: F 26 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: F 27 TYR cc_start: 0.8675 (m-80) cc_final: 0.8414 (m-80) REVERT: F 91 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.7888 (p0) REVERT: F 185 MET cc_start: 0.9132 (mpp) cc_final: 0.8566 (mpp) REVERT: F 213 GLU cc_start: 0.8218 (tp30) cc_final: 0.7715 (tp30) outliers start: 60 outliers final: 32 residues processed: 317 average time/residue: 0.0995 time to fit residues: 44.5005 Evaluate side-chains 295 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 K residue 79 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 55 ILE 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 44 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 59 VAL 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 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 120 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS K 79 GLN C 75 GLN C 115 ASN A 97 GLN B 115 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 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 = 0.3696 r_free = 0.3696 target = 0.088227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075163 restraints weight = 23820.274| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.24 r_work: 0.3315 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 10073 Z= 0.172 Angle : 0.664 14.742 13730 Z= 0.343 Chirality : 0.049 0.355 1521 Planarity : 0.004 0.046 1756 Dihedral : 4.770 20.742 1378 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.56 % Allowed : 21.11 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.23), residues: 1247 helix: 0.02 (0.36), residues: 217 sheet: -1.45 (0.23), residues: 405 loop : -1.32 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 118 TYR 0.018 0.001 TYR E 33 PHE 0.016 0.002 PHE D 113 TRP 0.020 0.002 TRP E 78 HIS 0.010 0.002 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00403 (10059) covalent geometry : angle 0.66027 (13702) SS BOND : bond 0.00535 ( 14) SS BOND : angle 1.73685 ( 28) hydrogen bonds : bond 0.03751 ( 330) hydrogen bonds : angle 5.97403 ( 906) *********************** 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 333 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 69 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8704 (mtmm) REVERT: C 36 ASP cc_start: 0.8713 (m-30) cc_final: 0.8232 (t0) REVERT: C 37 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 74 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8667 (mtmm) REVERT: C 82 PHE cc_start: 0.8609 (t80) cc_final: 0.8093 (t80) REVERT: C 83 LYS cc_start: 0.8589 (tmmt) cc_final: 0.8378 (tmmt) REVERT: C 84 GLU cc_start: 0.7731 (mp0) cc_final: 0.7350 (mp0) REVERT: C 91 TYR cc_start: 0.8936 (t80) cc_final: 0.8388 (t80) REVERT: H 38 MET cc_start: 0.8141 (ttt) cc_final: 0.7092 (tpp) REVERT: H 107 ASP cc_start: 0.8359 (t0) cc_final: 0.7878 (t0) REVERT: H 108 TYR cc_start: 0.8955 (m-80) cc_final: 0.8395 (m-80) REVERT: A 33 TYR cc_start: 0.8661 (p90) cc_final: 0.8312 (p90) REVERT: A 36 ASP cc_start: 0.8216 (m-30) cc_final: 0.7805 (t0) REVERT: A 41 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 137 LYS cc_start: 0.7971 (ptpt) cc_final: 0.7596 (mttm) REVERT: B 28 ASP cc_start: 0.8048 (m-30) cc_final: 0.7566 (m-30) REVERT: B 56 LYS cc_start: 0.8535 (ttmt) cc_final: 0.7883 (tttm) REVERT: B 75 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7823 (mm110) REVERT: B 83 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8091 (tptp) REVERT: B 87 ASP cc_start: 0.8911 (m-30) cc_final: 0.8445 (m-30) REVERT: B 125 LEU cc_start: 0.9178 (mp) cc_final: 0.8955 (mt) REVERT: D 49 THR cc_start: 0.8988 (p) cc_final: 0.8768 (t) REVERT: E 28 ASP cc_start: 0.8001 (m-30) cc_final: 0.7622 (m-30) REVERT: E 41 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8058 (mt-10) REVERT: E 56 LYS cc_start: 0.8720 (tttt) cc_final: 0.8413 (ttmt) REVERT: E 83 LYS cc_start: 0.9173 (tptp) cc_final: 0.8767 (tppt) REVERT: E 87 ASP cc_start: 0.8812 (m-30) cc_final: 0.8443 (m-30) REVERT: E 104 GLN cc_start: 0.7717 (tt0) cc_final: 0.7471 (mt0) REVERT: E 110 TYR cc_start: 0.8159 (t80) cc_final: 0.7815 (t80) REVERT: G 85 ARG cc_start: 0.8722 (mmm-85) cc_final: 0.7833 (mmm-85) REVERT: G 112 TYR cc_start: 0.8993 (t80) cc_final: 0.8631 (t80) REVERT: G 123 TYR cc_start: 0.8189 (m-10) cc_final: 0.7313 (m-10) REVERT: G 237 GLU cc_start: 0.7783 (tp30) cc_final: 0.7407 (tp30) REVERT: F 26 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: F 27 TYR cc_start: 0.8629 (m-80) cc_final: 0.8189 (m-80) REVERT: F 64 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8193 (m) REVERT: F 91 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.7551 (p0) REVERT: F 93 TYR cc_start: 0.8747 (m-80) cc_final: 0.8135 (m-80) REVERT: F 185 MET cc_start: 0.9018 (mpp) cc_final: 0.8523 (mpp) outliers start: 38 outliers final: 23 residues processed: 318 average time/residue: 0.0933 time to fit residues: 42.6410 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 : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 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 B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain E residue 58 VAL 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 64 VAL 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 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 95 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS E 75 GLN E 97 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS F 103 GLN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.089445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076398 restraints weight = 23853.655| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.24 r_work: 0.3346 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.7309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10073 Z= 0.156 Angle : 0.661 13.086 13730 Z= 0.338 Chirality : 0.050 0.299 1521 Planarity : 0.004 0.058 1756 Dihedral : 4.640 23.675 1378 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.10 % Allowed : 22.80 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.23), residues: 1247 helix: 0.15 (0.35), residues: 217 sheet: -1.35 (0.23), residues: 404 loop : -1.21 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 118 TYR 0.012 0.001 TYR E 33 PHE 0.016 0.002 PHE B 117 TRP 0.024 0.002 TRP E 78 HIS 0.008 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00365 (10059) covalent geometry : angle 0.65747 (13702) SS BOND : bond 0.00462 ( 14) SS BOND : angle 1.57167 ( 28) hydrogen bonds : bond 0.03577 ( 330) hydrogen bonds : angle 5.84777 ( 906) *********************** 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 325 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8654 (t) cc_final: 0.8136 (t) REVERT: K 69 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8645 (mtmm) REVERT: C 36 ASP cc_start: 0.8674 (m-30) cc_final: 0.8251 (t0) REVERT: C 37 GLU cc_start: 0.8719 (mm-30) cc_final: 0.7948 (mm-30) REVERT: C 41 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 74 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8596 (mtmm) REVERT: C 82 PHE cc_start: 0.8542 (t80) cc_final: 0.8013 (t80) REVERT: C 91 TYR cc_start: 0.8978 (t80) cc_final: 0.8465 (t80) REVERT: H 38 MET cc_start: 0.7606 (ttt) cc_final: 0.7225 (ttm) REVERT: H 81 MET cc_start: 0.8600 (ttt) cc_final: 0.8195 (ttp) REVERT: H 107 ASP cc_start: 0.8280 (t0) cc_final: 0.7476 (t0) REVERT: H 108 TYR cc_start: 0.8835 (m-80) cc_final: 0.8254 (m-80) REVERT: A 33 TYR cc_start: 0.8516 (p90) cc_final: 0.8181 (p90) REVERT: A 41 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7048 (mt-10) REVERT: A 137 LYS cc_start: 0.8028 (ptpt) cc_final: 0.7663 (mttm) REVERT: B 28 ASP cc_start: 0.7909 (m-30) cc_final: 0.7490 (m-30) REVERT: B 56 LYS cc_start: 0.8542 (ttmt) cc_final: 0.7905 (tttm) REVERT: B 75 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7876 (mm110) REVERT: B 83 LYS cc_start: 0.8889 (tmtt) cc_final: 0.7978 (tptp) REVERT: B 87 ASP cc_start: 0.8872 (m-30) cc_final: 0.8409 (m-30) REVERT: B 117 PHE cc_start: 0.8173 (m-10) cc_final: 0.7964 (m-10) REVERT: B 125 LEU cc_start: 0.9200 (mp) cc_final: 0.8988 (mt) REVERT: D 36 ASP cc_start: 0.8038 (t0) cc_final: 0.7769 (t0) REVERT: D 41 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8142 (mm-30) REVERT: D 88 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8333 (tp-100) REVERT: D 91 TYR cc_start: 0.8800 (t80) cc_final: 0.8322 (t80) REVERT: E 24 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: E 28 ASP cc_start: 0.8067 (m-30) cc_final: 0.7713 (m-30) REVERT: E 34 TYR cc_start: 0.8468 (m-80) cc_final: 0.8235 (m-80) REVERT: E 41 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8085 (mt-10) REVERT: E 56 LYS cc_start: 0.8743 (tttt) cc_final: 0.8474 (ttmt) REVERT: E 75 GLN cc_start: 0.8020 (mm110) cc_final: 0.7778 (mp10) REVERT: E 83 LYS cc_start: 0.9151 (tptp) cc_final: 0.8735 (tppt) REVERT: E 87 ASP cc_start: 0.8808 (m-30) cc_final: 0.8408 (m-30) REVERT: E 104 GLN cc_start: 0.7533 (tt0) cc_final: 0.7245 (mt0) REVERT: E 110 TYR cc_start: 0.8143 (t80) cc_final: 0.7795 (t80) REVERT: G 85 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.7858 (mmm-85) REVERT: G 112 TYR cc_start: 0.8950 (t80) cc_final: 0.8551 (t80) REVERT: G 123 TYR cc_start: 0.8294 (m-10) cc_final: 0.7437 (m-10) REVERT: G 237 GLU cc_start: 0.7738 (tp30) cc_final: 0.7281 (tp30) REVERT: F 26 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: F 27 TYR cc_start: 0.8475 (m-80) cc_final: 0.8171 (m-80) REVERT: F 64 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8109 (m) REVERT: F 91 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.7460 (p0) REVERT: F 93 TYR cc_start: 0.8718 (m-80) cc_final: 0.8170 (m-80) REVERT: F 185 MET cc_start: 0.8975 (mpp) cc_final: 0.8488 (mpp) REVERT: F 204 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7466 (mt-10) outliers start: 33 outliers final: 23 residues processed: 311 average time/residue: 0.0943 time to fit residues: 42.1249 Evaluate side-chains 295 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 B residue 75 GLN Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 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 3 optimal weight: 0.0870 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN 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 = 0.3746 r_free = 0.3746 target = 0.090655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077726 restraints weight = 23896.019| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.24 r_work: 0.3374 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10073 Z= 0.145 Angle : 0.675 12.047 13730 Z= 0.342 Chirality : 0.049 0.275 1521 Planarity : 0.004 0.056 1756 Dihedral : 4.577 22.368 1378 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.19 % Allowed : 23.45 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.23), residues: 1247 helix: 0.21 (0.36), residues: 217 sheet: -1.18 (0.24), residues: 404 loop : -1.09 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 118 TYR 0.013 0.001 TYR E 33 PHE 0.027 0.002 PHE A 53 TRP 0.028 0.002 TRP E 78 HIS 0.010 0.001 HIS K 28 Details of bonding type rmsd covalent geometry : bond 0.00338 (10059) covalent geometry : angle 0.67137 (13702) SS BOND : bond 0.00434 ( 14) SS BOND : angle 1.68458 ( 28) hydrogen bonds : bond 0.03442 ( 330) hydrogen bonds : angle 5.77065 ( 906) *********************** 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 324 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 0.356 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: 0.8787 (t) cc_final: 0.8273 (t) REVERT: C 36 ASP cc_start: 0.8698 (m-30) cc_final: 0.8279 (t0) REVERT: C 37 GLU cc_start: 0.8668 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 82 PHE cc_start: 0.8555 (t80) cc_final: 0.8086 (t80) REVERT: C 83 LYS cc_start: 0.8637 (tmmt) cc_final: 0.8404 (tmmt) REVERT: C 84 GLU cc_start: 0.7914 (mp0) cc_final: 0.7666 (mp0) REVERT: C 91 TYR cc_start: 0.8944 (t80) cc_final: 0.8434 (t80) REVERT: H 4 LEU cc_start: 0.8805 (mm) cc_final: 0.8337 (mm) REVERT: H 52 ASP cc_start: 0.8049 (t0) cc_final: 0.7342 (t0) REVERT: H 57 ASP cc_start: 0.8397 (m-30) cc_final: 0.8077 (p0) REVERT: H 81 MET cc_start: 0.8453 (ttt) cc_final: 0.8101 (ttp) REVERT: H 107 ASP cc_start: 0.8092 (t0) cc_final: 0.6904 (t0) REVERT: H 108 TYR cc_start: 0.8787 (m-80) cc_final: 0.7990 (m-80) REVERT: A 36 ASP cc_start: 0.8234 (t0) cc_final: 0.7993 (t70) REVERT: A 41 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7048 (mt-10) REVERT: A 137 LYS cc_start: 0.8231 (ptpt) cc_final: 0.7836 (mttp) REVERT: B 28 ASP cc_start: 0.7886 (m-30) cc_final: 0.7605 (m-30) REVERT: B 56 LYS cc_start: 0.8547 (ttmt) cc_final: 0.7925 (tttm) REVERT: B 75 GLN cc_start: 0.8109 (tp40) cc_final: 0.7816 (mm110) REVERT: B 83 LYS cc_start: 0.8956 (tmtt) cc_final: 0.8151 (tptp) REVERT: B 87 ASP cc_start: 0.8890 (m-30) cc_final: 0.8446 (m-30) REVERT: B 110 TYR cc_start: 0.8716 (t80) cc_final: 0.8502 (t80) REVERT: D 36 ASP cc_start: 0.8190 (t0) cc_final: 0.7821 (t0) REVERT: D 41 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8058 (mm-30) REVERT: D 48 ASP cc_start: 0.8951 (m-30) cc_final: 0.8620 (p0) REVERT: D 84 GLU cc_start: 0.8210 (mp0) cc_final: 0.7779 (mp0) REVERT: D 88 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8349 (tp-100) REVERT: D 91 TYR cc_start: 0.8831 (t80) cc_final: 0.8332 (t80) REVERT: E 24 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: E 28 ASP cc_start: 0.8069 (m-30) cc_final: 0.7724 (m-30) REVERT: E 34 TYR cc_start: 0.8413 (m-80) cc_final: 0.8188 (m-80) REVERT: E 41 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8065 (mt-10) REVERT: E 56 LYS cc_start: 0.8834 (tttt) cc_final: 0.8501 (ttmt) REVERT: E 83 LYS cc_start: 0.9182 (tptp) cc_final: 0.8712 (tppt) REVERT: E 87 ASP cc_start: 0.8778 (m-30) cc_final: 0.8369 (m-30) REVERT: E 104 GLN cc_start: 0.7417 (tt0) cc_final: 0.7138 (mt0) REVERT: E 110 TYR cc_start: 0.8086 (t80) cc_final: 0.7725 (t80) REVERT: G 112 TYR cc_start: 0.8926 (t80) cc_final: 0.8544 (t80) REVERT: F 26 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: F 64 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8073 (m) REVERT: F 91 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.7378 (p0) REVERT: F 93 TYR cc_start: 0.8641 (m-80) cc_final: 0.8144 (m-80) REVERT: F 185 MET cc_start: 0.8972 (mpp) cc_final: 0.8487 (mpp) outliers start: 34 outliers final: 22 residues processed: 314 average time/residue: 0.0984 time to fit residues: 43.9817 Evaluate side-chains 294 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 71 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 99 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 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 34 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 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 103 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS H 6 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.088442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075210 restraints weight = 23881.751| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.27 r_work: 0.3326 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.7589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10073 Z= 0.195 Angle : 0.694 12.048 13730 Z= 0.356 Chirality : 0.050 0.290 1521 Planarity : 0.005 0.067 1756 Dihedral : 4.709 24.170 1378 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.47 % Allowed : 23.55 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.23), residues: 1247 helix: 0.01 (0.35), residues: 223 sheet: -1.14 (0.24), residues: 409 loop : -1.06 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 118 TYR 0.021 0.001 TYR C 34 PHE 0.026 0.002 PHE A 53 TRP 0.039 0.002 TRP E 78 HIS 0.008 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00448 (10059) covalent geometry : angle 0.69138 (13702) SS BOND : bond 0.00431 ( 14) SS BOND : angle 1.58284 ( 28) hydrogen bonds : bond 0.03772 ( 330) hydrogen bonds : angle 5.84287 ( 906) *********************** 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 310 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7872 (tp) REVERT: K 49 SER cc_start: 0.8767 (t) cc_final: 0.8282 (t) REVERT: C 36 ASP cc_start: 0.8598 (m-30) cc_final: 0.8198 (t0) REVERT: C 37 GLU cc_start: 0.8711 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 83 LYS cc_start: 0.8655 (tmmt) cc_final: 0.8384 (tmmt) REVERT: C 84 GLU cc_start: 0.7904 (mp0) cc_final: 0.7672 (mp0) REVERT: C 91 TYR cc_start: 0.9043 (t80) cc_final: 0.8515 (t80) REVERT: H 4 LEU cc_start: 0.8753 (mm) cc_final: 0.8368 (mm) REVERT: H 52 ASP cc_start: 0.8234 (t0) cc_final: 0.7984 (t0) REVERT: H 67 LYS cc_start: 0.9001 (ptpt) cc_final: 0.8743 (tptt) REVERT: H 81 MET cc_start: 0.8472 (ttt) cc_final: 0.8123 (ttp) REVERT: H 106 MET cc_start: 0.8289 (mmm) cc_final: 0.7093 (mtt) REVERT: H 107 ASP cc_start: 0.8192 (t0) cc_final: 0.6979 (t0) REVERT: H 108 TYR cc_start: 0.8825 (m-80) cc_final: 0.7871 (m-80) REVERT: A 36 ASP cc_start: 0.8306 (t0) cc_final: 0.8041 (t70) REVERT: A 41 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7108 (mt-10) REVERT: A 75 GLN cc_start: 0.8659 (mt0) cc_final: 0.8418 (mm-40) REVERT: A 84 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 115 ASN cc_start: 0.8811 (m-40) cc_final: 0.8348 (p0) REVERT: A 137 LYS cc_start: 0.8003 (ptpt) cc_final: 0.7731 (mttp) REVERT: B 56 LYS cc_start: 0.8625 (ttmt) cc_final: 0.7998 (tttm) REVERT: B 75 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7962 (mm110) REVERT: B 83 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8271 (tptp) REVERT: B 87 ASP cc_start: 0.8886 (m-30) cc_final: 0.8431 (m-30) REVERT: D 36 ASP cc_start: 0.8323 (t0) cc_final: 0.8037 (t0) REVERT: D 41 GLU cc_start: 0.8735 (mm-30) cc_final: 0.7971 (mm-30) REVERT: D 48 ASP cc_start: 0.8976 (m-30) cc_final: 0.8637 (p0) REVERT: D 84 GLU cc_start: 0.8216 (mp0) cc_final: 0.7695 (mp0) REVERT: D 91 TYR cc_start: 0.8871 (t80) cc_final: 0.8355 (t80) REVERT: E 24 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7724 (tp30) REVERT: E 28 ASP cc_start: 0.8030 (m-30) cc_final: 0.7690 (m-30) REVERT: E 34 TYR cc_start: 0.8492 (m-80) cc_final: 0.8163 (m-80) REVERT: E 41 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7910 (mt-10) REVERT: E 56 LYS cc_start: 0.8760 (tttt) cc_final: 0.8402 (ttpt) REVERT: E 83 LYS cc_start: 0.9210 (tptp) cc_final: 0.8715 (tppt) REVERT: E 87 ASP cc_start: 0.8871 (m-30) cc_final: 0.8439 (m-30) REVERT: E 91 TYR cc_start: 0.8419 (t80) cc_final: 0.8013 (t80) REVERT: E 110 TYR cc_start: 0.8250 (t80) cc_final: 0.7865 (t80) REVERT: G 112 TYR cc_start: 0.8971 (t80) cc_final: 0.8596 (t80) REVERT: F 26 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: F 64 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8127 (m) REVERT: F 91 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.7447 (p0) REVERT: F 93 TYR cc_start: 0.8694 (m-80) cc_final: 0.8135 (m-80) REVERT: F 185 MET cc_start: 0.8993 (mpp) cc_final: 0.8501 (mpp) REVERT: F 208 MET cc_start: 0.6905 (mmm) cc_final: 0.6640 (mmm) outliers start: 37 outliers final: 23 residues processed: 298 average time/residue: 0.0924 time to fit residues: 39.4233 Evaluate side-chains 285 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 65 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 58 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 34 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 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 103 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS D 88 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.089255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075622 restraints weight = 23910.496| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.42 r_work: 0.3328 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10073 Z= 0.185 Angle : 0.705 11.764 13730 Z= 0.361 Chirality : 0.050 0.293 1521 Planarity : 0.005 0.054 1756 Dihedral : 4.727 22.473 1378 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.28 % Allowed : 23.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.24), residues: 1247 helix: 0.02 (0.35), residues: 222 sheet: -1.11 (0.24), residues: 409 loop : -1.05 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 118 TYR 0.015 0.001 TYR C 34 PHE 0.025 0.002 PHE A 53 TRP 0.046 0.002 TRP E 78 HIS 0.007 0.001 HIS K 28 Details of bonding type rmsd covalent geometry : bond 0.00429 (10059) covalent geometry : angle 0.70273 (13702) SS BOND : bond 0.00442 ( 14) SS BOND : angle 1.54084 ( 28) hydrogen bonds : bond 0.03677 ( 330) hydrogen bonds : angle 5.82318 ( 906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8779 (t) cc_final: 0.8262 (t) REVERT: C 33 TYR cc_start: 0.8354 (p90) cc_final: 0.8052 (p90) REVERT: C 36 ASP cc_start: 0.8661 (m-30) cc_final: 0.8215 (t0) REVERT: C 37 GLU cc_start: 0.8704 (mm-30) cc_final: 0.7848 (mm-30) REVERT: C 83 LYS cc_start: 0.8705 (tmmt) cc_final: 0.8362 (tmmt) REVERT: C 91 TYR cc_start: 0.9057 (t80) cc_final: 0.8481 (t80) REVERT: H 4 LEU cc_start: 0.8719 (mm) cc_final: 0.8357 (mm) REVERT: H 36 TRP cc_start: 0.8626 (m100) cc_final: 0.7694 (m100) REVERT: H 38 MET cc_start: 0.7946 (tpp) cc_final: 0.7343 (mmm) REVERT: H 52 ASP cc_start: 0.8365 (t0) cc_final: 0.7540 (t0) REVERT: H 57 ASP cc_start: 0.8471 (m-30) cc_final: 0.7987 (p0) REVERT: H 67 LYS cc_start: 0.8941 (ptpt) cc_final: 0.8668 (tptt) REVERT: H 81 MET cc_start: 0.8389 (ttt) cc_final: 0.8018 (ttp) REVERT: H 94 TYR cc_start: 0.8609 (m-80) cc_final: 0.8165 (m-80) REVERT: H 106 MET cc_start: 0.8258 (mmm) cc_final: 0.7248 (mtt) REVERT: H 107 ASP cc_start: 0.8189 (t0) cc_final: 0.6908 (t0) REVERT: H 108 TYR cc_start: 0.8793 (m-80) cc_final: 0.7816 (m-80) REVERT: A 36 ASP cc_start: 0.8373 (t0) cc_final: 0.8091 (t70) REVERT: A 41 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 75 GLN cc_start: 0.8578 (mt0) cc_final: 0.8357 (mm-40) REVERT: A 84 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 115 ASN cc_start: 0.8840 (m-40) cc_final: 0.8394 (p0) REVERT: A 137 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7850 (mttp) REVERT: B 56 LYS cc_start: 0.8607 (ttmt) cc_final: 0.7947 (tttm) REVERT: B 75 GLN cc_start: 0.8366 (tp40) cc_final: 0.7980 (mm110) REVERT: B 83 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8161 (tptp) REVERT: B 87 ASP cc_start: 0.8911 (m-30) cc_final: 0.8438 (m-30) REVERT: D 36 ASP cc_start: 0.8428 (t0) cc_final: 0.8115 (t0) REVERT: D 41 GLU cc_start: 0.8664 (mm-30) cc_final: 0.7861 (mm-30) REVERT: D 84 GLU cc_start: 0.8221 (mp0) cc_final: 0.7685 (mp0) REVERT: D 91 TYR cc_start: 0.8864 (t80) cc_final: 0.8408 (t80) REVERT: E 24 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: E 28 ASP cc_start: 0.8083 (m-30) cc_final: 0.7735 (m-30) REVERT: E 34 TYR cc_start: 0.8532 (m-80) cc_final: 0.8173 (m-80) REVERT: E 41 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 56 LYS cc_start: 0.8751 (tttt) cc_final: 0.8376 (ttpt) REVERT: E 83 LYS cc_start: 0.9240 (tptp) cc_final: 0.8679 (tppt) REVERT: E 87 ASP cc_start: 0.8894 (m-30) cc_final: 0.8413 (m-30) REVERT: E 91 TYR cc_start: 0.8384 (t80) cc_final: 0.7980 (t80) REVERT: E 110 TYR cc_start: 0.8271 (t80) cc_final: 0.7903 (t80) REVERT: G 112 TYR cc_start: 0.8993 (t80) cc_final: 0.8613 (t80) REVERT: G 202 PRO cc_start: 0.9205 (Cg_exo) cc_final: 0.8909 (Cg_endo) REVERT: F 26 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: F 64 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (m) REVERT: F 91 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.7378 (p0) REVERT: F 93 TYR cc_start: 0.8766 (m-80) cc_final: 0.8190 (m-80) REVERT: F 185 MET cc_start: 0.9055 (mpp) cc_final: 0.8545 (mpp) REVERT: F 204 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7587 (mm-30) REVERT: F 208 MET cc_start: 0.6913 (mmm) cc_final: 0.6654 (mmm) REVERT: F 210 GLU cc_start: 0.7160 (pm20) cc_final: 0.6324 (pm20) outliers start: 35 outliers final: 24 residues processed: 288 average time/residue: 0.0959 time to fit residues: 39.8293 Evaluate side-chains 282 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR 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 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 B residue 65 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 58 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 34 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 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 98 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 28 HIS D 97 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN 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 = 0.3719 r_free = 0.3719 target = 0.088797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075176 restraints weight = 23862.441| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.36 r_work: 0.3324 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.7830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10073 Z= 0.197 Angle : 0.720 11.641 13730 Z= 0.370 Chirality : 0.050 0.303 1521 Planarity : 0.005 0.053 1756 Dihedral : 4.768 22.891 1378 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.10 % Allowed : 24.39 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.24), residues: 1247 helix: -0.04 (0.35), residues: 221 sheet: -1.10 (0.24), residues: 409 loop : -1.03 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 118 TYR 0.014 0.001 TYR E 33 PHE 0.024 0.002 PHE A 53 TRP 0.027 0.002 TRP E 78 HIS 0.008 0.001 HIS K 28 Details of bonding type rmsd covalent geometry : bond 0.00457 (10059) covalent geometry : angle 0.71712 (13702) SS BOND : bond 0.00427 ( 14) SS BOND : angle 1.53083 ( 28) hydrogen bonds : bond 0.03734 ( 330) hydrogen bonds : angle 5.83439 ( 906) ********************** 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 294 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 49 SER cc_start: 0.8784 (t) cc_final: 0.7802 (t) REVERT: C 33 TYR cc_start: 0.8323 (p90) cc_final: 0.8012 (p90) REVERT: C 36 ASP cc_start: 0.8605 (m-30) cc_final: 0.8197 (t0) REVERT: C 37 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7829 (mm-30) REVERT: C 91 TYR cc_start: 0.9055 (t80) cc_final: 0.8489 (t80) REVERT: H 4 LEU cc_start: 0.8732 (mm) cc_final: 0.8368 (mm) REVERT: H 36 TRP cc_start: 0.8711 (m100) cc_final: 0.7646 (m100) REVERT: H 38 MET cc_start: 0.7925 (tpp) cc_final: 0.7457 (mmm) REVERT: H 52 ASP cc_start: 0.8504 (t0) cc_final: 0.7675 (t0) REVERT: H 57 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7804 (p0) REVERT: H 67 LYS cc_start: 0.8906 (ptpt) cc_final: 0.8677 (tptt) REVERT: H 69 THR cc_start: 0.8607 (p) cc_final: 0.8363 (p) REVERT: H 81 MET cc_start: 0.8411 (ttt) cc_final: 0.8128 (ttp) REVERT: H 82 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8260 (tp30) REVERT: H 94 TYR cc_start: 0.8601 (m-80) cc_final: 0.8110 (m-80) REVERT: H 106 MET cc_start: 0.8325 (mmm) cc_final: 0.7308 (mtt) REVERT: H 107 ASP cc_start: 0.8179 (t0) cc_final: 0.6925 (t0) REVERT: H 108 TYR cc_start: 0.8778 (m-80) cc_final: 0.7836 (m-80) REVERT: A 36 ASP cc_start: 0.8313 (t0) cc_final: 0.8001 (t70) REVERT: A 41 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 75 GLN cc_start: 0.8575 (mt0) cc_final: 0.8328 (mm-40) REVERT: A 115 ASN cc_start: 0.8810 (m-40) cc_final: 0.8382 (p0) REVERT: A 137 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7853 (mttp) REVERT: B 56 LYS cc_start: 0.8611 (ttmt) cc_final: 0.7955 (tttm) REVERT: B 75 GLN cc_start: 0.8332 (tp40) cc_final: 0.7954 (mm110) REVERT: B 83 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8444 (tptp) REVERT: B 110 TYR cc_start: 0.8834 (t80) cc_final: 0.8593 (t80) REVERT: D 36 ASP cc_start: 0.8397 (t0) cc_final: 0.8166 (t0) REVERT: D 41 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7867 (mm-30) REVERT: D 84 GLU cc_start: 0.8230 (mp0) cc_final: 0.7692 (mp0) REVERT: D 91 TYR cc_start: 0.8870 (t80) cc_final: 0.8508 (t80) REVERT: E 28 ASP cc_start: 0.7994 (m-30) cc_final: 0.7660 (m-30) REVERT: E 34 TYR cc_start: 0.8556 (m-80) cc_final: 0.8217 (m-80) REVERT: E 41 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7861 (mt-10) REVERT: E 56 LYS cc_start: 0.8805 (tttt) cc_final: 0.8456 (ttpt) REVERT: E 83 LYS cc_start: 0.9225 (tptp) cc_final: 0.8658 (tppt) REVERT: E 87 ASP cc_start: 0.8861 (m-30) cc_final: 0.8356 (m-30) REVERT: E 91 TYR cc_start: 0.8384 (t80) cc_final: 0.7978 (t80) REVERT: E 110 TYR cc_start: 0.8284 (t80) cc_final: 0.7895 (t80) REVERT: G 112 TYR cc_start: 0.8982 (t80) cc_final: 0.8610 (t80) REVERT: G 202 PRO cc_start: 0.9199 (Cg_exo) cc_final: 0.8911 (Cg_endo) REVERT: F 26 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: F 64 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8170 (m) REVERT: F 91 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.7392 (p0) REVERT: F 93 TYR cc_start: 0.8747 (m-80) cc_final: 0.8169 (m-80) REVERT: F 185 MET cc_start: 0.9035 (mpp) cc_final: 0.8535 (mpp) REVERT: F 204 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7578 (mm-30) REVERT: F 208 MET cc_start: 0.6945 (mmm) cc_final: 0.6684 (mmm) REVERT: F 210 GLU cc_start: 0.7141 (pm20) cc_final: 0.6274 (pm20) REVERT: F 213 GLU cc_start: 0.8353 (tp30) cc_final: 0.7785 (mm-30) outliers start: 33 outliers final: 25 residues processed: 283 average time/residue: 0.0938 time to fit residues: 38.0524 Evaluate side-chains 280 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR 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 113 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 B residue 65 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 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 107 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 99 optimal weight: 0.0270 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.088790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075182 restraints weight = 24051.001| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.38 r_work: 0.3323 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.204 10073 Z= 0.242 Angle : 1.010 59.164 13730 Z= 0.569 Chirality : 0.051 0.412 1521 Planarity : 0.006 0.079 1756 Dihedral : 4.741 22.988 1378 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.19 % Allowed : 24.86 % Favored : 71.95 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.24), residues: 1247 helix: -0.04 (0.35), residues: 221 sheet: -1.10 (0.24), residues: 407 loop : -1.02 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 119 TYR 0.013 0.001 TYR E 33 PHE 0.032 0.002 PHE B 53 TRP 0.026 0.002 TRP E 78 HIS 0.110 0.004 HIS K 28 Details of bonding type rmsd covalent geometry : bond 0.00550 (10059) covalent geometry : angle 1.00871 (13702) SS BOND : bond 0.00422 ( 14) SS BOND : angle 1.51224 ( 28) hydrogen bonds : bond 0.03734 ( 330) hydrogen bonds : angle 5.84330 ( 906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2293.53 seconds wall clock time: 40 minutes 31.90 seconds (2431.90 seconds total)