Starting phenix.real_space_refine on Thu Mar 5 10:35:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x6o_33024/03_2026/7x6o_33024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6o_33024/03_2026/7x6o_33024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x6o_33024/03_2026/7x6o_33024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6o_33024/03_2026/7x6o_33024.map" model { file = "/net/cci-nas-00/data/ceres_data/7x6o_33024/03_2026/7x6o_33024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6o_33024/03_2026/7x6o_33024.cif" } resolution = 3.5 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= 0.002 sd= 0.032 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 96 5.16 5 C 13581 2.51 5 N 3678 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21609 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "C" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "I" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "K" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "H" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "J" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 4.70, per 1000 atoms: 0.22 Number of scatterers: 21609 At special positions: 0 Unit cell: (185.838, 176.612, 142.344, 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 96 16.00 O 4254 8.00 N 3678 7.00 C 13581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 107 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 313 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 102 " - pdb=" SG CYS I 107 " distance=2.03 Simple disulfide: pdb=" SG CYS I 157 " - pdb=" SG CYS I 213 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 100 " - pdb=" SG CYS F 146 " distance=2.03 Simple disulfide: pdb=" SG CYS F 289 " - pdb=" SG CYS F 313 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 102 " - pdb=" SG CYS J 107 " distance=2.03 Simple disulfide: pdb=" SG CYS J 157 " - pdb=" SG CYS J 213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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: 1.54 Conformation dependent library (CDL) restraints added in 1.0 seconds 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 60 sheets defined 15.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.610A pdb=" N LEU A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.830A pdb=" N GLU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.675A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.510A pdb=" N GLN A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 53 removed outlier: 3.541A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 124 removed outlier: 3.941A pdb=" N LEU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.620A pdb=" N VAL B 152 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.799A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR C 91 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.963A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.643A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 183 through 187 removed outlier: 3.818A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 187' Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.606A pdb=" N LEU E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.777A pdb=" N GLU E 78 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 removed outlier: 3.667A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 removed outlier: 3.540A pdb=" N GLN E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 53 Processing helix chain 'G' and resid 74 through 124 removed outlier: 3.790A pdb=" N LEU G 80 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 96 " --> pdb=" O TRP G 92 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.643A pdb=" N VAL G 152 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 153 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 removed outlier: 3.628A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 166 " --> pdb=" O TYR G 162 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.788A pdb=" N THR I 91 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.671A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 126' Processing helix chain 'K' and resid 183 through 189 removed outlier: 3.799A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 183 through 189' Processing helix chain 'K' and resid 212 through 214 No H-bonds generated for 'chain 'K' and resid 212 through 214' Processing helix chain 'F' and resid 66 through 72 removed outlier: 3.623A pdb=" N LEU F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 removed outlier: 3.729A pdb=" N GLU F 78 " --> pdb=" O PRO F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 115 removed outlier: 3.669A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 removed outlier: 3.532A pdb=" N GLN F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 53 Processing helix chain 'H' and resid 74 through 124 removed outlier: 3.804A pdb=" N LEU H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY H 87 " --> pdb=" O LYS H 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 96 " --> pdb=" O TRP H 92 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.648A pdb=" N VAL H 152 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS H 153 " --> pdb=" O MET H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 removed outlier: 3.773A pdb=" N TYR H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA H 166 " --> pdb=" O TYR H 162 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.791A pdb=" N THR J 91 " --> pdb=" O ASP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 204 through 206 No H-bonds generated for 'chain 'J' and resid 204 through 206' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.965A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.623A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 121 through 126' Processing helix chain 'L' and resid 183 through 187 removed outlier: 3.804A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 removed outlier: 3.509A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 14 " --> pdb=" O HIS B 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 139 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.453A pdb=" N LEU A 51 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR A 287 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS A 53 " --> pdb=" O THR A 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61 removed outlier: 7.699A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.514A pdb=" N ALA A 266 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 186 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.514A pdb=" N ALA A 266 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 171 through 176 removed outlier: 3.514A pdb=" N ALA A 254 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 175 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 211 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 294 through 296 removed outlier: 3.651A pdb=" N THR A 291 " --> pdb=" O GLY A 294 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 296 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 289 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR B 64 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.878A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.928A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.928A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 97 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 98 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY C 116 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 193 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 198 " --> pdb=" O HIS C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 193 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 167 through 171 removed outlier: 3.746A pdb=" N TYR C 211 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.513A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.454A pdb=" N VAL D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 49 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.639A pdb=" N ASN D 137 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 145 through 150 removed outlier: 3.641A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 149 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR D 192 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 32 through 36 removed outlier: 3.528A pdb=" N GLY G 33 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS E 14 " --> pdb=" O HIS G 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 139 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.559A pdb=" N LEU E 51 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS E 285 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 60 through 61 removed outlier: 7.683A pdb=" N LEU E 60 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.586A pdb=" N ALA E 266 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU E 186 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.586A pdb=" N ALA E 266 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 171 through 176 removed outlier: 3.619A pdb=" N TYR E 175 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 211 " --> pdb=" O LYS E 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 294 through 296 removed outlier: 3.531A pdb=" N THR E 291 " --> pdb=" O GLY E 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 296 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS E 289 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 310 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR G 64 " --> pdb=" O GLY E 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.868A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.842A pdb=" N GLY I 10 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 127 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 12 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.842A pdb=" N GLY I 10 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 127 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 12 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 97 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG I 98 " --> pdb=" O ASP I 118 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY I 116 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.609A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL I 198 " --> pdb=" O HIS I 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.609A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 167 through 171 removed outlier: 3.793A pdb=" N TYR I 211 " --> pdb=" O VAL I 228 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.637A pdb=" N SER K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.535A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 49 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.642A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN K 138 " --> pdb=" O TYR K 173 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 145 through 150 removed outlier: 3.607A pdb=" N LYS K 145 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS K 149 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR K 192 " --> pdb=" O PHE K 209 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL K 205 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 32 through 36 removed outlier: 3.534A pdb=" N GLY H 33 " --> pdb=" O HIS H 26 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS F 14 " --> pdb=" O HIS H 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 139 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AE7, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AE8, first strand: chain 'F' and resid 43 through 44 removed outlier: 3.535A pdb=" N GLU F 44 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 51 through 54 removed outlier: 7.479A pdb=" N LEU F 51 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR F 287 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LYS F 53 " --> pdb=" O THR F 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 60 through 61 removed outlier: 7.689A pdb=" N LEU F 60 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.545A pdb=" N ALA F 266 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU F 186 " --> pdb=" O PRO F 261 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.545A pdb=" N ALA F 266 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 171 through 176 removed outlier: 3.507A pdb=" N ALA F 254 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR F 175 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 211 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 294 through 296 removed outlier: 3.638A pdb=" N THR F 291 " --> pdb=" O GLY F 294 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE F 296 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS F 289 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 310 " --> pdb=" O GLN F 290 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR H 64 " --> pdb=" O GLY F 311 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.840A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.885A pdb=" N GLY J 10 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR J 127 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 12 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 124 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.885A pdb=" N GLY J 10 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR J 127 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 12 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 124 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 97 " --> pdb=" O ASN J 35 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG J 98 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY J 116 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 137 through 140 removed outlier: 3.642A pdb=" N SER J 197 " --> pdb=" O CYS J 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 193 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL J 198 " --> pdb=" O HIS J 181 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 137 through 140 removed outlier: 3.642A pdb=" N SER J 197 " --> pdb=" O CYS J 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 193 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 167 through 171 removed outlier: 3.745A pdb=" N TYR J 211 " --> pdb=" O VAL J 228 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.548A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.499A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR L 49 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.655A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.645A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 1950 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: 4.21 Time building geometry restraints manager: 2.16 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: 7002 1.34 - 1.46: 5243 1.46 - 1.58: 9730 1.58 - 1.70: 0 1.70 - 1.81: 123 Bond restraints: 22098 Sorted by residual: bond pdb=" N SER A 299 " pdb=" CA SER A 299 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 bond pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.24e+00 bond pdb=" N SER F 299 " pdb=" CA SER F 299 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.22e+00 bond pdb=" C THR F 298 " pdb=" N SER F 299 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.40e-02 5.10e+03 2.84e+00 bond pdb=" C THR E 298 " pdb=" N SER E 299 " ideal model delta sigma weight residual 1.329 1.352 -0.023 1.40e-02 5.10e+03 2.66e+00 ... (remaining 22093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 29839 2.69 - 5.37: 139 5.37 - 8.06: 10 8.06 - 10.75: 0 10.75 - 13.44: 3 Bond angle restraints: 29991 Sorted by residual: angle pdb=" C THR E 298 " pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta sigma weight residual 121.70 135.14 -13.44 1.80e+00 3.09e-01 5.57e+01 angle pdb=" C THR F 298 " pdb=" N SER F 299 " pdb=" CA SER F 299 " ideal model delta sigma weight residual 121.70 135.10 -13.40 1.80e+00 3.09e-01 5.54e+01 angle pdb=" C THR A 298 " pdb=" N SER A 299 " pdb=" CA SER A 299 " ideal model delta sigma weight residual 121.70 134.87 -13.17 1.80e+00 3.09e-01 5.36e+01 angle pdb=" N VAL G 66 " pdb=" CA VAL G 66 " pdb=" C VAL G 66 " ideal model delta sigma weight residual 111.81 108.61 3.20 8.60e-01 1.35e+00 1.38e+01 angle pdb=" N VAL B 66 " pdb=" CA VAL B 66 " pdb=" C VAL B 66 " ideal model delta sigma weight residual 111.81 108.73 3.08 8.60e-01 1.35e+00 1.28e+01 ... (remaining 29986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 12644 14.70 - 29.41: 414 29.41 - 44.11: 135 44.11 - 58.82: 16 58.82 - 73.52: 3 Dihedral angle restraints: 13212 sinusoidal: 5163 harmonic: 8049 Sorted by residual: dihedral pdb=" CA HIS G 72 " pdb=" C HIS G 72 " pdb=" N LEU G 73 " pdb=" CA LEU G 73 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N LEU B 73 " pdb=" CA LEU B 73 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA HIS H 72 " pdb=" C HIS H 72 " pdb=" N LEU H 73 " pdb=" CA LEU H 73 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 13209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2504 0.041 - 0.081: 504 0.081 - 0.122: 286 0.122 - 0.162: 18 0.162 - 0.203: 3 Chirality restraints: 3315 Sorted by residual: chirality pdb=" CA SER F 299 " pdb=" N SER F 299 " pdb=" C SER F 299 " pdb=" CB SER F 299 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA SER E 299 " pdb=" N SER E 299 " pdb=" C SER E 299 " pdb=" CB SER E 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA SER A 299 " pdb=" N SER A 299 " pdb=" C SER A 299 " pdb=" CB SER A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 3312 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K 79 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO K 80 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 80 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO L 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 80 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " -0.026 5.00e-02 4.00e+02 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5723 2.81 - 3.33: 16250 3.33 - 3.85: 36637 3.85 - 4.38: 39644 4.38 - 4.90: 70741 Nonbonded interactions: 168995 Sorted by model distance: nonbonded pdb=" OG1 THR E 287 " pdb=" O ILE E 296 " model vdw 2.283 3.040 nonbonded pdb=" O LEU B 89 " pdb=" OG1 THR B 93 " model vdw 2.311 3.040 nonbonded pdb=" O CYS A 52 " pdb=" OH TYR A 88 " model vdw 2.312 3.040 nonbonded pdb=" O LEU H 89 " pdb=" OG1 THR H 93 " model vdw 2.314 3.040 nonbonded pdb=" O LEU G 89 " pdb=" OG1 THR G 93 " model vdw 2.319 3.040 ... (remaining 168990 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 0.690 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.180 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 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 0.040 22128 Z= 0.115 Angle : 0.487 13.437 30051 Z= 0.280 Chirality : 0.042 0.203 3315 Planarity : 0.005 0.049 3864 Dihedral : 8.088 73.519 7980 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.82 % Allowed : 3.31 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.13), residues: 2757 helix: -4.02 (0.11), residues: 300 sheet: -1.37 (0.17), residues: 822 loop : -2.03 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.009 0.001 TYR F 88 PHE 0.013 0.001 PHE A 154 TRP 0.006 0.001 TRP F 86 HIS 0.005 0.000 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00211 (22098) covalent geometry : angle 0.48741 (29991) SS BOND : bond 0.00107 ( 30) SS BOND : angle 0.41683 ( 60) hydrogen bonds : bond 0.31192 ( 676) hydrogen bonds : angle 10.82961 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 527 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7396 (mp) cc_final: 0.7109 (mt) REVERT: A 90 VAL cc_start: 0.5771 (t) cc_final: 0.5550 (t) REVERT: A 108 TYR cc_start: 0.7161 (t80) cc_final: 0.6655 (t80) REVERT: A 133 TRP cc_start: 0.5698 (m-90) cc_final: 0.5073 (m-90) REVERT: A 170 LYS cc_start: 0.7683 (tttt) cc_final: 0.7269 (mmtt) REVERT: A 175 TYR cc_start: 0.6765 (t80) cc_final: 0.6497 (t80) REVERT: A 231 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7693 (ttt-90) REVERT: A 233 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6344 (mm-40) REVERT: A 293 LYS cc_start: 0.7106 (mttt) cc_final: 0.6827 (mttt) REVERT: B 81 ASN cc_start: 0.7458 (t0) cc_final: 0.7245 (t0) REVERT: B 103 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6223 (mm-30) REVERT: B 110 TYR cc_start: 0.7095 (t80) cc_final: 0.6747 (t80) REVERT: B 149 MET cc_start: 0.5695 (mmt) cc_final: 0.5389 (mmm) REVERT: B 150 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7023 (mm-30) REVERT: B 152 VAL cc_start: 0.6773 (t) cc_final: 0.6451 (m) REVERT: B 153 LYS cc_start: 0.6736 (ttpt) cc_final: 0.6419 (ttpt) REVERT: C 25 SER cc_start: 0.6975 (p) cc_final: 0.6768 (m) REVERT: C 36 TRP cc_start: 0.5129 (m100) cc_final: 0.4845 (m100) REVERT: C 67 ARG cc_start: 0.6312 (mtm180) cc_final: 0.6073 (mtm180) REVERT: D 4 MET cc_start: 0.5388 (mmm) cc_final: 0.4729 (mmm) REVERT: D 36 TYR cc_start: 0.4375 (m-80) cc_final: 0.4130 (m-80) REVERT: D 82 ASP cc_start: 0.6356 (m-30) cc_final: 0.5142 (m-30) REVERT: E 217 SER cc_start: 0.6550 (m) cc_final: 0.5919 (p) REVERT: E 231 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7390 (mtp-110) REVERT: E 249 LYS cc_start: 0.6322 (ttpt) cc_final: 0.5878 (ttmm) REVERT: E 267 MET cc_start: 0.5526 (ppp) cc_final: 0.5188 (ppp) REVERT: G 40 SER cc_start: 0.8776 (m) cc_final: 0.8373 (p) REVERT: G 53 ASN cc_start: 0.7116 (m-40) cc_final: 0.6803 (m-40) REVERT: G 81 ASN cc_start: 0.7269 (t0) cc_final: 0.7035 (t0) REVERT: G 131 LYS cc_start: 0.7249 (tttt) cc_final: 0.7049 (tttt) REVERT: I 67 ARG cc_start: 0.6780 (mtm180) cc_final: 0.6365 (mtm180) REVERT: I 115 TYR cc_start: 0.6761 (m-80) cc_final: 0.6165 (m-80) REVERT: I 163 PHE cc_start: 0.5121 (t80) cc_final: 0.4845 (t80) REVERT: K 4 MET cc_start: 0.5849 (mmm) cc_final: 0.4715 (ttt) REVERT: K 5 THR cc_start: 0.6528 (m) cc_final: 0.6320 (t) REVERT: K 37 GLN cc_start: 0.7607 (tt0) cc_final: 0.7041 (tt0) REVERT: K 63 SER cc_start: 0.7054 (t) cc_final: 0.6827 (t) REVERT: K 82 ASP cc_start: 0.6077 (m-30) cc_final: 0.4199 (m-30) REVERT: F 108 TYR cc_start: 0.6935 (t80) cc_final: 0.6696 (t80) REVERT: F 170 LYS cc_start: 0.7852 (tttt) cc_final: 0.7424 (mptt) REVERT: F 179 LYS cc_start: 0.7010 (mmtt) cc_final: 0.6677 (mttp) REVERT: F 191 HIS cc_start: 0.5112 (m-70) cc_final: 0.4739 (m-70) REVERT: F 312 LYS cc_start: 0.7113 (mttt) cc_final: 0.6665 (mmtt) REVERT: F 321 LYS cc_start: 0.7113 (pttt) cc_final: 0.6902 (tppt) REVERT: F 322 LEU cc_start: 0.8057 (mt) cc_final: 0.7789 (mt) REVERT: F 323 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6997 (ttt90) REVERT: H 131 LYS cc_start: 0.7329 (tttt) cc_final: 0.7017 (tttt) REVERT: H 149 MET cc_start: 0.5754 (mmt) cc_final: 0.5504 (mmp) REVERT: L 4 MET cc_start: 0.5946 (mmm) cc_final: 0.5184 (tpp) REVERT: L 37 GLN cc_start: 0.7502 (tt0) cc_final: 0.6756 (tt0) REVERT: L 82 ASP cc_start: 0.6256 (m-30) cc_final: 0.6044 (m-30) REVERT: L 97 THR cc_start: 0.7518 (m) cc_final: 0.7203 (p) outliers start: 44 outliers final: 10 residues processed: 560 average time/residue: 0.1437 time to fit residues: 126.8040 Evaluate side-chains 442 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 432 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 25 HIS B 50 ASN B 62 GLN B 95 ASN B 142 HIS E 233 GLN G 25 HIS G 62 GLN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN H 25 HIS H 81 ASN H 95 ASN ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.237004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.203094 restraints weight = 35341.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.208932 restraints weight = 18087.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.212524 restraints weight = 10670.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.214770 restraints weight = 7113.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.216144 restraints weight = 5254.208| |-----------------------------------------------------------------------------| r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22128 Z= 0.151 Angle : 0.599 10.282 30051 Z= 0.317 Chirality : 0.045 0.227 3315 Planarity : 0.004 0.059 3864 Dihedral : 4.041 56.923 3020 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.95 % Allowed : 8.28 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.14), residues: 2757 helix: -1.69 (0.23), residues: 294 sheet: -0.88 (0.17), residues: 825 loop : -1.40 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 61 TYR 0.020 0.002 TYR C 112 PHE 0.028 0.002 PHE A 154 TRP 0.023 0.002 TRP K 148 HIS 0.005 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00325 (22098) covalent geometry : angle 0.59504 (29991) SS BOND : bond 0.00321 ( 30) SS BOND : angle 1.73346 ( 60) hydrogen bonds : bond 0.05511 ( 676) hydrogen bonds : angle 6.77017 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 475 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.6492 (t80) cc_final: 0.5821 (t80) REVERT: A 170 LYS cc_start: 0.7766 (tttt) cc_final: 0.7322 (mmtt) REVERT: A 175 TYR cc_start: 0.6710 (t80) cc_final: 0.6406 (t80) REVERT: A 321 LYS cc_start: 0.7044 (tptt) cc_final: 0.6791 (tptt) REVERT: B 103 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6524 (mm-30) REVERT: B 110 TYR cc_start: 0.7019 (t80) cc_final: 0.6698 (t80) REVERT: B 131 LYS cc_start: 0.7205 (tttt) cc_final: 0.6921 (tttt) REVERT: B 140 PHE cc_start: 0.5291 (m-80) cc_final: 0.4870 (m-80) REVERT: B 153 LYS cc_start: 0.7291 (ttpt) cc_final: 0.6830 (mttt) REVERT: C 27 PHE cc_start: 0.6360 (p90) cc_final: 0.5999 (p90) REVERT: C 67 ARG cc_start: 0.6568 (mtm180) cc_final: 0.6224 (mtm180) REVERT: D 6 GLN cc_start: 0.5952 (mp10) cc_final: 0.5707 (mp10) REVERT: D 36 TYR cc_start: 0.4938 (m-80) cc_final: 0.4558 (m-80) REVERT: D 81 GLU cc_start: 0.6571 (pm20) cc_final: 0.6273 (pm20) REVERT: D 82 ASP cc_start: 0.6464 (m-30) cc_final: 0.5626 (m-30) REVERT: E 70 TRP cc_start: 0.6658 (t60) cc_final: 0.6363 (t60) REVERT: E 122 GLU cc_start: 0.6673 (tt0) cc_final: 0.6368 (tt0) REVERT: E 231 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7432 (mtp-110) REVERT: E 318 LYS cc_start: 0.6893 (mtmt) cc_final: 0.6632 (pttt) REVERT: G 40 SER cc_start: 0.8613 (m) cc_final: 0.8376 (p) REVERT: G 41 THR cc_start: 0.8420 (m) cc_final: 0.7879 (p) REVERT: I 29 PHE cc_start: 0.6450 (t80) cc_final: 0.6227 (t80) REVERT: I 67 ARG cc_start: 0.7017 (mtm180) cc_final: 0.6511 (mtm180) REVERT: I 112 TYR cc_start: 0.6342 (m-80) cc_final: 0.5518 (m-10) REVERT: I 115 TYR cc_start: 0.6841 (m-80) cc_final: 0.6434 (m-80) REVERT: I 163 PHE cc_start: 0.5228 (t80) cc_final: 0.4925 (t80) REVERT: K 4 MET cc_start: 0.4656 (mmm) cc_final: 0.4314 (ttt) REVERT: K 37 GLN cc_start: 0.7129 (tt0) cc_final: 0.6721 (tt0) REVERT: K 82 ASP cc_start: 0.5623 (m-30) cc_final: 0.5268 (m-30) REVERT: F 42 LEU cc_start: 0.7785 (mp) cc_final: 0.7526 (mt) REVERT: F 170 LYS cc_start: 0.7916 (tttt) cc_final: 0.7631 (mptt) REVERT: F 179 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6850 (mttt) REVERT: F 191 HIS cc_start: 0.5364 (m-70) cc_final: 0.5049 (m-70) REVERT: F 321 LYS cc_start: 0.7608 (pttt) cc_final: 0.7292 (tppt) REVERT: F 322 LEU cc_start: 0.8181 (mt) cc_final: 0.7567 (mm) REVERT: H 40 SER cc_start: 0.8506 (m) cc_final: 0.8253 (p) REVERT: H 51 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7680 (ttmt) REVERT: H 103 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6253 (mm-30) REVERT: H 131 LYS cc_start: 0.7342 (tttt) cc_final: 0.7141 (tttt) REVERT: J 104 SER cc_start: 0.7302 (p) cc_final: 0.6808 (t) REVERT: L 4 MET cc_start: 0.5229 (mmm) cc_final: 0.4870 (ttm) REVERT: L 37 GLN cc_start: 0.7290 (tt0) cc_final: 0.6462 (tt0) REVERT: L 82 ASP cc_start: 0.6262 (m-30) cc_final: 0.5768 (m-30) REVERT: L 94 PHE cc_start: 0.6584 (p90) cc_final: 0.6272 (p90) REVERT: L 97 THR cc_start: 0.7214 (m) cc_final: 0.6972 (p) outliers start: 47 outliers final: 27 residues processed: 505 average time/residue: 0.1518 time to fit residues: 117.9591 Evaluate side-chains 475 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 448 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 32 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN A 306 HIS B 50 ASN B 62 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN E 203 GLN E 233 GLN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN H 53 ASN H 81 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 106 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.228545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.194110 restraints weight = 35195.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.199843 restraints weight = 18229.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.203460 restraints weight = 10923.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.205769 restraints weight = 7326.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.207056 restraints weight = 5389.799| |-----------------------------------------------------------------------------| r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22128 Z= 0.188 Angle : 0.634 11.165 30051 Z= 0.331 Chirality : 0.045 0.227 3315 Planarity : 0.004 0.042 3864 Dihedral : 4.173 55.186 3012 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.48 % Allowed : 9.44 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 2757 helix: -0.88 (0.26), residues: 297 sheet: -0.51 (0.17), residues: 834 loop : -1.13 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 61 TYR 0.027 0.002 TYR A 88 PHE 0.025 0.002 PHE A 154 TRP 0.033 0.002 TRP H 14 HIS 0.006 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00399 (22098) covalent geometry : angle 0.63002 (29991) SS BOND : bond 0.00533 ( 30) SS BOND : angle 1.62788 ( 60) hydrogen bonds : bond 0.04978 ( 676) hydrogen bonds : angle 6.09721 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 457 time to evaluate : 0.495 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: A 170 LYS cc_start: 0.7837 (tttt) cc_final: 0.7380 (mmtt) REVERT: A 175 TYR cc_start: 0.6669 (t80) cc_final: 0.6401 (t80) REVERT: A 293 LYS cc_start: 0.6811 (mttt) cc_final: 0.6500 (mttt) REVERT: A 312 LYS cc_start: 0.7455 (mttt) cc_final: 0.7149 (mttt) REVERT: A 319 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7914 (p) REVERT: A 321 LYS cc_start: 0.7244 (tptt) cc_final: 0.6964 (tptt) REVERT: B 42 GLN cc_start: 0.7271 (tp40) cc_final: 0.7030 (tp-100) REVERT: B 103 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6597 (mm-30) REVERT: B 110 TYR cc_start: 0.7069 (t80) cc_final: 0.6820 (t80) REVERT: B 114 ASN cc_start: 0.6985 (m-40) cc_final: 0.6486 (m110) REVERT: B 131 LYS cc_start: 0.7262 (tttt) cc_final: 0.6913 (tttt) REVERT: B 140 PHE cc_start: 0.5640 (m-80) cc_final: 0.5433 (m-80) REVERT: C 67 ARG cc_start: 0.6899 (mtm180) cc_final: 0.6584 (mtm180) REVERT: D 81 GLU cc_start: 0.6746 (pm20) cc_final: 0.6422 (pm20) REVERT: D 82 ASP cc_start: 0.6863 (m-30) cc_final: 0.5816 (m-30) REVERT: E 70 TRP cc_start: 0.6864 (t60) cc_final: 0.6635 (t60) REVERT: E 122 GLU cc_start: 0.6975 (tt0) cc_final: 0.6747 (tt0) REVERT: E 123 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.7140 (ttm170) REVERT: E 315 LYS cc_start: 0.3638 (mttt) cc_final: 0.3336 (mttt) REVERT: G 40 SER cc_start: 0.8458 (m) cc_final: 0.8253 (p) REVERT: G 41 THR cc_start: 0.8460 (m) cc_final: 0.7959 (p) REVERT: G 103 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6853 (mm-30) REVERT: G 149 MET cc_start: 0.5840 (mmp) cc_final: 0.5595 (mmm) REVERT: I 29 PHE cc_start: 0.6546 (t80) cc_final: 0.6267 (t80) REVERT: I 67 ARG cc_start: 0.7175 (mtm180) cc_final: 0.6757 (mtm180) REVERT: I 112 TYR cc_start: 0.6100 (m-80) cc_final: 0.5485 (m-10) REVERT: I 115 TYR cc_start: 0.7121 (m-80) cc_final: 0.6719 (m-80) REVERT: I 163 PHE cc_start: 0.5372 (t80) cc_final: 0.5025 (t80) REVERT: K 4 MET cc_start: 0.4472 (mmm) cc_final: 0.3900 (ttt) REVERT: K 6 GLN cc_start: 0.6254 (mp10) cc_final: 0.5429 (mp10) REVERT: K 53 ARG cc_start: 0.6728 (mtp85) cc_final: 0.6428 (mtp85) REVERT: K 82 ASP cc_start: 0.6083 (m-30) cc_final: 0.5760 (m-30) REVERT: F 110 GLU cc_start: 0.3310 (OUTLIER) cc_final: 0.3019 (mt-10) REVERT: F 170 LYS cc_start: 0.8014 (tttt) cc_final: 0.7632 (tttt) REVERT: F 179 LYS cc_start: 0.7320 (mmtt) cc_final: 0.6966 (mttt) REVERT: F 191 HIS cc_start: 0.5713 (m-70) cc_final: 0.4984 (m-70) REVERT: F 210 PHE cc_start: 0.6393 (t80) cc_final: 0.6170 (t80) REVERT: F 312 LYS cc_start: 0.7030 (mttt) cc_final: 0.6770 (mmtm) REVERT: F 321 LYS cc_start: 0.7784 (pttt) cc_final: 0.7496 (tppt) REVERT: F 322 LEU cc_start: 0.8217 (mt) cc_final: 0.8014 (mt) REVERT: H 51 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7494 (ttmt) REVERT: H 92 TRP cc_start: 0.4785 (m-10) cc_final: 0.3702 (m-90) REVERT: H 103 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6145 (mm-30) REVERT: H 118 LEU cc_start: 0.8188 (mm) cc_final: 0.7844 (mm) REVERT: J 163 PHE cc_start: 0.5460 (t80) cc_final: 0.5164 (t80) REVERT: L 37 GLN cc_start: 0.7393 (tt0) cc_final: 0.6526 (tt0) REVERT: L 81 GLU cc_start: 0.7386 (pt0) cc_final: 0.6632 (pm20) REVERT: L 94 PHE cc_start: 0.6743 (p90) cc_final: 0.6468 (p90) REVERT: L 97 THR cc_start: 0.7194 (m) cc_final: 0.6868 (p) outliers start: 60 outliers final: 33 residues processed: 490 average time/residue: 0.1532 time to fit residues: 114.7366 Evaluate side-chains 478 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 443 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN A 290 GLN B 62 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN E 233 GLN E 290 GLN G 53 ASN G 79 ASN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN F 290 GLN H 79 ASN H 81 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.223374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.188326 restraints weight = 34694.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.194130 restraints weight = 17940.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.197720 restraints weight = 10691.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.199965 restraints weight = 7150.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.201375 restraints weight = 5253.952| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22128 Z= 0.243 Angle : 0.700 10.533 30051 Z= 0.364 Chirality : 0.048 0.235 3315 Planarity : 0.004 0.046 3864 Dihedral : 4.550 36.938 3008 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.82 % Allowed : 10.35 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.15), residues: 2757 helix: -0.88 (0.26), residues: 279 sheet: -0.28 (0.18), residues: 831 loop : -0.97 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 61 TYR 0.029 0.002 TYR E 88 PHE 0.047 0.002 PHE C 29 TRP 0.049 0.003 TRP F 70 HIS 0.009 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00517 (22098) covalent geometry : angle 0.69584 (29991) SS BOND : bond 0.00484 ( 30) SS BOND : angle 1.88828 ( 60) hydrogen bonds : bond 0.05177 ( 676) hydrogen bonds : angle 6.17219 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 458 time to evaluate : 0.665 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: A 170 LYS cc_start: 0.7913 (tttt) cc_final: 0.7479 (mmtt) REVERT: A 175 TYR cc_start: 0.6689 (t80) cc_final: 0.6401 (t80) REVERT: A 177 ASN cc_start: 0.7323 (t0) cc_final: 0.7032 (t0) REVERT: A 179 LYS cc_start: 0.6658 (tttp) cc_final: 0.6383 (tttp) REVERT: A 293 LYS cc_start: 0.7309 (mttt) cc_final: 0.6891 (mttt) REVERT: A 312 LYS cc_start: 0.7569 (mttt) cc_final: 0.7276 (mttt) REVERT: A 319 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8180 (p) REVERT: B 68 LYS cc_start: 0.8221 (mtmm) cc_final: 0.8020 (mtmm) REVERT: B 90 ASP cc_start: 0.6514 (m-30) cc_final: 0.6299 (m-30) REVERT: B 103 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 110 TYR cc_start: 0.7094 (t80) cc_final: 0.6801 (t80) REVERT: B 114 ASN cc_start: 0.6920 (m-40) cc_final: 0.6201 (m-40) REVERT: B 131 LYS cc_start: 0.7327 (tttt) cc_final: 0.6933 (tttt) REVERT: B 149 MET cc_start: 0.5717 (mmp) cc_final: 0.5336 (mmp) REVERT: B 158 ASP cc_start: 0.7184 (t0) cc_final: 0.6717 (t0) REVERT: C 103 SER cc_start: 0.7380 (p) cc_final: 0.7029 (p) REVERT: D 53 ARG cc_start: 0.6665 (mtp85) cc_final: 0.5924 (mtp85) REVERT: D 81 GLU cc_start: 0.6822 (pm20) cc_final: 0.6477 (pm20) REVERT: D 82 ASP cc_start: 0.7040 (m-30) cc_final: 0.5895 (m-30) REVERT: E 122 GLU cc_start: 0.7240 (tt0) cc_final: 0.6983 (tt0) REVERT: E 231 ARG cc_start: 0.8083 (mtt-85) cc_final: 0.7407 (mtp-110) REVERT: E 315 LYS cc_start: 0.4130 (mttt) cc_final: 0.3842 (mttt) REVERT: G 40 SER cc_start: 0.8576 (m) cc_final: 0.8375 (p) REVERT: G 58 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7477 (mmtp) REVERT: G 95 ASN cc_start: 0.8253 (t0) cc_final: 0.8030 (t0) REVERT: G 103 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7061 (mm-30) REVERT: G 121 LYS cc_start: 0.8084 (tttt) cc_final: 0.7767 (tmtt) REVERT: I 29 PHE cc_start: 0.6844 (t80) cc_final: 0.6497 (t80) REVERT: I 115 TYR cc_start: 0.7036 (m-80) cc_final: 0.6655 (m-80) REVERT: I 163 PHE cc_start: 0.5562 (t80) cc_final: 0.5210 (t80) REVERT: K 36 TYR cc_start: 0.5301 (m-80) cc_final: 0.4591 (m-80) REVERT: K 61 ARG cc_start: 0.7412 (mtm110) cc_final: 0.6839 (ttp-110) REVERT: K 82 ASP cc_start: 0.6554 (m-30) cc_final: 0.5817 (m-30) REVERT: F 70 TRP cc_start: 0.6431 (t60) cc_final: 0.5914 (t60) REVERT: F 121 PHE cc_start: 0.6388 (t80) cc_final: 0.5972 (t80) REVERT: F 160 TRP cc_start: 0.6595 (OUTLIER) cc_final: 0.6381 (m100) REVERT: F 170 LYS cc_start: 0.8085 (tttt) cc_final: 0.7713 (tttt) REVERT: F 179 LYS cc_start: 0.7460 (mmtt) cc_final: 0.7129 (mttt) REVERT: F 191 HIS cc_start: 0.5631 (m-70) cc_final: 0.4961 (m-70) REVERT: F 210 PHE cc_start: 0.6463 (t80) cc_final: 0.6183 (t80) REVERT: F 321 LYS cc_start: 0.7995 (pttt) cc_final: 0.7650 (tppt) REVERT: F 322 LEU cc_start: 0.8190 (mt) cc_final: 0.7929 (mt) REVERT: F 323 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7252 (mtt-85) REVERT: H 51 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7567 (ttpt) REVERT: H 59 MET cc_start: 0.7165 (tmm) cc_final: 0.6961 (tmm) REVERT: H 73 LEU cc_start: 0.6543 (mt) cc_final: 0.6329 (mt) REVERT: H 103 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6135 (mm-30) REVERT: H 118 LEU cc_start: 0.8057 (mm) cc_final: 0.6957 (mm) REVERT: H 131 LYS cc_start: 0.7307 (tttt) cc_final: 0.6948 (tttt) REVERT: H 149 MET cc_start: 0.6533 (mmp) cc_final: 0.6292 (mmp) REVERT: J 163 PHE cc_start: 0.5690 (t80) cc_final: 0.5386 (t80) REVERT: L 81 GLU cc_start: 0.7534 (pt0) cc_final: 0.6775 (pm20) REVERT: L 97 THR cc_start: 0.7245 (m) cc_final: 0.6911 (p) outliers start: 68 outliers final: 44 residues processed: 492 average time/residue: 0.1508 time to fit residues: 114.1034 Evaluate side-chains 484 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 438 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 160 TRP Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 255 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 211 optimal weight: 0.9980 chunk 92 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN B 42 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN H 53 ASN H 60 ASN H 81 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.224322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.188441 restraints weight = 34616.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.194299 restraints weight = 17626.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.197947 restraints weight = 10519.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.200219 restraints weight = 7038.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.201670 restraints weight = 5204.280| |-----------------------------------------------------------------------------| r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22128 Z= 0.135 Angle : 0.606 10.611 30051 Z= 0.313 Chirality : 0.045 0.213 3315 Planarity : 0.004 0.043 3864 Dihedral : 4.211 38.404 3005 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.40 % Allowed : 12.51 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 2757 helix: -0.61 (0.27), residues: 288 sheet: 0.16 (0.19), residues: 768 loop : -0.83 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 61 TYR 0.031 0.002 TYR A 108 PHE 0.040 0.002 PHE C 29 TRP 0.040 0.002 TRP B 14 HIS 0.007 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00295 (22098) covalent geometry : angle 0.60360 (29991) SS BOND : bond 0.00260 ( 30) SS BOND : angle 1.44279 ( 60) hydrogen bonds : bond 0.04361 ( 676) hydrogen bonds : angle 5.84885 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 447 time to evaluate : 0.779 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: A 170 LYS cc_start: 0.7819 (tttt) cc_final: 0.7381 (mmtt) REVERT: A 175 TYR cc_start: 0.6667 (t80) cc_final: 0.6366 (t80) REVERT: A 177 ASN cc_start: 0.7160 (t0) cc_final: 0.6780 (t0) REVERT: A 179 LYS cc_start: 0.6721 (tttp) cc_final: 0.6383 (tttp) REVERT: A 234 GLU cc_start: 0.5470 (pm20) cc_final: 0.5154 (pm20) REVERT: A 293 LYS cc_start: 0.7116 (mttt) cc_final: 0.6703 (mttt) REVERT: A 319 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8182 (p) REVERT: A 321 LYS cc_start: 0.7412 (tptt) cc_final: 0.7084 (tptt) REVERT: B 68 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7948 (mtmm) REVERT: B 82 LYS cc_start: 0.8424 (pttt) cc_final: 0.8012 (pttm) REVERT: B 103 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6951 (mm-30) REVERT: B 110 TYR cc_start: 0.7077 (t80) cc_final: 0.6654 (t80) REVERT: B 114 ASN cc_start: 0.6863 (m-40) cc_final: 0.6149 (m-40) REVERT: B 131 LYS cc_start: 0.7255 (tttt) cc_final: 0.6868 (tttt) REVERT: C 70 ILE cc_start: 0.4536 (OUTLIER) cc_final: 0.4037 (tp) REVERT: C 122 GLN cc_start: 0.6009 (mm-40) cc_final: 0.5787 (mm-40) REVERT: D 81 GLU cc_start: 0.6796 (pm20) cc_final: 0.6427 (pm20) REVERT: D 82 ASP cc_start: 0.7047 (m-30) cc_final: 0.6049 (m-30) REVERT: E 231 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7449 (mtp-110) REVERT: E 267 MET cc_start: 0.6745 (ppp) cc_final: 0.5841 (ppp) REVERT: E 315 LYS cc_start: 0.4022 (mttt) cc_final: 0.3612 (mtmt) REVERT: G 80 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6195 (tt) REVERT: G 81 ASN cc_start: 0.8149 (t0) cc_final: 0.7881 (t0) REVERT: G 95 ASN cc_start: 0.8195 (t0) cc_final: 0.7972 (t0) REVERT: G 103 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6948 (mm-30) REVERT: I 29 PHE cc_start: 0.6782 (t80) cc_final: 0.6415 (t80) REVERT: I 115 TYR cc_start: 0.7039 (m-80) cc_final: 0.6543 (m-80) REVERT: K 36 TYR cc_start: 0.5168 (m-80) cc_final: 0.4434 (m-80) REVERT: K 61 ARG cc_start: 0.7336 (mtm110) cc_final: 0.6996 (ttp-110) REVERT: K 82 ASP cc_start: 0.6420 (m-30) cc_final: 0.5878 (m-30) REVERT: F 160 TRP cc_start: 0.6465 (OUTLIER) cc_final: 0.6218 (m100) REVERT: F 170 LYS cc_start: 0.8065 (tttt) cc_final: 0.7681 (tttt) REVERT: F 179 LYS cc_start: 0.7402 (mmtt) cc_final: 0.7060 (mttt) REVERT: F 191 HIS cc_start: 0.5523 (m-70) cc_final: 0.4878 (m-70) REVERT: F 210 PHE cc_start: 0.6396 (t80) cc_final: 0.6114 (t80) REVERT: F 321 LYS cc_start: 0.8040 (pttt) cc_final: 0.7656 (tppt) REVERT: F 323 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.6704 (mtm-85) REVERT: H 51 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7434 (ttmt) REVERT: H 59 MET cc_start: 0.7175 (tmm) cc_final: 0.6785 (tmm) REVERT: H 73 LEU cc_start: 0.6517 (mt) cc_final: 0.6314 (mt) REVERT: H 103 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6316 (mm-30) REVERT: H 131 LYS cc_start: 0.7280 (tttt) cc_final: 0.6919 (tttt) REVERT: H 153 LYS cc_start: 0.7146 (ptpp) cc_final: 0.6857 (mtmm) REVERT: J 163 PHE cc_start: 0.5755 (t80) cc_final: 0.5434 (t80) REVERT: L 81 GLU cc_start: 0.7586 (pt0) cc_final: 0.6770 (pm20) REVERT: L 97 THR cc_start: 0.7124 (m) cc_final: 0.6875 (p) outliers start: 58 outliers final: 36 residues processed: 481 average time/residue: 0.1555 time to fit residues: 115.0173 Evaluate side-chains 464 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 424 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 173 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 245 optimal weight: 40.0000 chunk 169 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 271 optimal weight: 20.0000 chunk 221 optimal weight: 0.0970 chunk 206 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.225995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.190464 restraints weight = 34261.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.196240 restraints weight = 17649.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.199915 restraints weight = 10639.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.202201 restraints weight = 7165.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.203625 restraints weight = 5314.124| |-----------------------------------------------------------------------------| r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22128 Z= 0.132 Angle : 0.599 10.557 30051 Z= 0.310 Chirality : 0.044 0.207 3315 Planarity : 0.004 0.046 3864 Dihedral : 4.171 37.610 3005 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.24 % Allowed : 13.50 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2757 helix: -0.69 (0.27), residues: 306 sheet: 0.47 (0.19), residues: 732 loop : -0.75 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 61 TYR 0.027 0.002 TYR A 108 PHE 0.033 0.002 PHE C 29 TRP 0.046 0.002 TRP F 70 HIS 0.007 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00289 (22098) covalent geometry : angle 0.59653 (29991) SS BOND : bond 0.00381 ( 30) SS BOND : angle 1.44026 ( 60) hydrogen bonds : bond 0.04180 ( 676) hydrogen bonds : angle 5.74992 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 433 time to evaluate : 0.763 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: A 123 ARG cc_start: 0.7265 (ttm170) cc_final: 0.7048 (ttm110) REVERT: A 170 LYS cc_start: 0.7720 (tttt) cc_final: 0.7370 (mmtt) REVERT: A 175 TYR cc_start: 0.6667 (t80) cc_final: 0.6377 (t80) REVERT: A 293 LYS cc_start: 0.7120 (mttt) cc_final: 0.6701 (mttt) REVERT: A 318 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7166 (ttmt) REVERT: A 319 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8195 (p) REVERT: B 110 TYR cc_start: 0.7091 (t80) cc_final: 0.6725 (t80) REVERT: B 114 ASN cc_start: 0.6945 (m-40) cc_final: 0.6072 (m-40) REVERT: B 131 LYS cc_start: 0.7260 (tttt) cc_final: 0.6859 (tttt) REVERT: C 122 GLN cc_start: 0.6207 (mm-40) cc_final: 0.5999 (mm-40) REVERT: D 81 GLU cc_start: 0.6794 (pm20) cc_final: 0.6417 (pm20) REVERT: D 82 ASP cc_start: 0.7069 (m-30) cc_final: 0.6053 (m-30) REVERT: E 231 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7561 (mtp-110) REVERT: E 267 MET cc_start: 0.6749 (ppp) cc_final: 0.5825 (ppp) REVERT: E 315 LYS cc_start: 0.4103 (mttt) cc_final: 0.3617 (mtpt) REVERT: G 17 MET cc_start: 0.6577 (ttp) cc_final: 0.6236 (ttp) REVERT: G 103 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6975 (mm-30) REVERT: G 149 MET cc_start: 0.5853 (mmm) cc_final: 0.5387 (mmm) REVERT: I 29 PHE cc_start: 0.6823 (t80) cc_final: 0.6457 (t80) REVERT: I 115 TYR cc_start: 0.7008 (m-80) cc_final: 0.6495 (m-80) REVERT: K 4 MET cc_start: 0.5087 (ttm) cc_final: 0.4864 (ttm) REVERT: K 36 TYR cc_start: 0.4969 (m-80) cc_final: 0.4239 (m-80) REVERT: K 61 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7175 (ttp-110) REVERT: K 82 ASP cc_start: 0.6551 (m-30) cc_final: 0.6065 (m-30) REVERT: F 160 TRP cc_start: 0.6489 (OUTLIER) cc_final: 0.6251 (m100) REVERT: F 170 LYS cc_start: 0.8098 (tttt) cc_final: 0.7689 (tttt) REVERT: F 179 LYS cc_start: 0.7400 (mmtt) cc_final: 0.7066 (mttt) REVERT: F 191 HIS cc_start: 0.5553 (m-70) cc_final: 0.4942 (m-70) REVERT: F 210 PHE cc_start: 0.6408 (t80) cc_final: 0.6111 (t80) REVERT: F 321 LYS cc_start: 0.8079 (pttt) cc_final: 0.7655 (tppt) REVERT: F 323 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7279 (mtt-85) REVERT: H 51 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7358 (ttpt) REVERT: H 59 MET cc_start: 0.7148 (tmm) cc_final: 0.6700 (tmm) REVERT: H 73 LEU cc_start: 0.6529 (mt) cc_final: 0.6319 (mt) REVERT: H 103 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6276 (mm-30) REVERT: H 131 LYS cc_start: 0.7229 (tttt) cc_final: 0.6847 (tttt) REVERT: J 163 PHE cc_start: 0.5773 (t80) cc_final: 0.5431 (t80) REVERT: L 81 GLU cc_start: 0.7630 (pt0) cc_final: 0.6788 (pm20) REVERT: L 97 THR cc_start: 0.7075 (m) cc_final: 0.6813 (p) outliers start: 54 outliers final: 40 residues processed: 466 average time/residue: 0.1553 time to fit residues: 111.4078 Evaluate side-chains 462 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 419 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain G residue 14 TRP Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 242 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN C 106 ASN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.222630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.187597 restraints weight = 33736.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.193197 restraints weight = 17487.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.196714 restraints weight = 10471.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.198868 restraints weight = 7017.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.200167 restraints weight = 5183.182| |-----------------------------------------------------------------------------| r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22128 Z= 0.165 Angle : 0.624 10.357 30051 Z= 0.323 Chirality : 0.045 0.207 3315 Planarity : 0.004 0.048 3864 Dihedral : 4.322 38.399 3005 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.57 % Allowed : 13.71 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2757 helix: -0.49 (0.28), residues: 288 sheet: 0.30 (0.19), residues: 780 loop : -0.72 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 61 TYR 0.027 0.002 TYR A 108 PHE 0.033 0.002 PHE F 154 TRP 0.039 0.002 TRP F 70 HIS 0.009 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00356 (22098) covalent geometry : angle 0.62084 (29991) SS BOND : bond 0.00324 ( 30) SS BOND : angle 1.49943 ( 60) hydrogen bonds : bond 0.04372 ( 676) hydrogen bonds : angle 5.76915 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 440 time to evaluate : 0.683 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: A 170 LYS cc_start: 0.7724 (tttt) cc_final: 0.7374 (mmtt) REVERT: A 171 LEU cc_start: 0.7530 (mt) cc_final: 0.7177 (tp) REVERT: A 175 TYR cc_start: 0.6666 (t80) cc_final: 0.6383 (t80) REVERT: A 293 LYS cc_start: 0.7187 (mttt) cc_final: 0.6769 (mttt) REVERT: A 312 LYS cc_start: 0.7290 (mttt) cc_final: 0.6850 (mptt) REVERT: A 318 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7328 (ttmt) REVERT: A 319 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8248 (p) REVERT: A 321 LYS cc_start: 0.7327 (tptt) cc_final: 0.7006 (tptt) REVERT: B 74 GLU cc_start: 0.5411 (mp0) cc_final: 0.5186 (mp0) REVERT: B 82 LYS cc_start: 0.8416 (pttt) cc_final: 0.8054 (pttp) REVERT: B 110 TYR cc_start: 0.7018 (t80) cc_final: 0.6708 (t80) REVERT: B 131 LYS cc_start: 0.7369 (tttt) cc_final: 0.6962 (tttt) REVERT: B 149 MET cc_start: 0.6012 (mmp) cc_final: 0.5770 (mmp) REVERT: C 36 TRP cc_start: 0.5943 (m100) cc_final: 0.5227 (m100) REVERT: C 67 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6749 (mtm180) REVERT: C 70 ILE cc_start: 0.4782 (OUTLIER) cc_final: 0.4442 (tp) REVERT: C 122 GLN cc_start: 0.6096 (mm-40) cc_final: 0.5867 (mm-40) REVERT: D 81 GLU cc_start: 0.6924 (pm20) cc_final: 0.6567 (pm20) REVERT: D 82 ASP cc_start: 0.7148 (m-30) cc_final: 0.6111 (m-30) REVERT: E 112 ARG cc_start: 0.6896 (mtp180) cc_final: 0.5643 (ttp80) REVERT: E 231 ARG cc_start: 0.8112 (mtt-85) cc_final: 0.7557 (mtp-110) REVERT: E 267 MET cc_start: 0.6728 (ppp) cc_final: 0.5754 (ppp) REVERT: E 278 SER cc_start: 0.7041 (OUTLIER) cc_final: 0.6671 (p) REVERT: E 315 LYS cc_start: 0.4442 (mttt) cc_final: 0.3046 (mttt) REVERT: E 323 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.7341 (mmm160) REVERT: G 17 MET cc_start: 0.6580 (ttp) cc_final: 0.6273 (ttp) REVERT: G 103 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6936 (mm-30) REVERT: G 121 LYS cc_start: 0.7942 (tttt) cc_final: 0.7654 (tmtt) REVERT: G 149 MET cc_start: 0.6066 (mmm) cc_final: 0.5651 (mmm) REVERT: G 158 ASP cc_start: 0.7088 (t0) cc_final: 0.6761 (t0) REVERT: I 29 PHE cc_start: 0.6790 (t80) cc_final: 0.6547 (t80) REVERT: I 36 TRP cc_start: 0.4981 (m100) cc_final: 0.4561 (m100) REVERT: K 36 TYR cc_start: 0.5082 (m-80) cc_final: 0.4284 (m-80) REVERT: K 61 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7137 (ttp-110) REVERT: K 82 ASP cc_start: 0.6895 (m-30) cc_final: 0.6246 (m-30) REVERT: F 123 ARG cc_start: 0.7290 (ttp80) cc_final: 0.7090 (ttp80) REVERT: F 160 TRP cc_start: 0.6542 (OUTLIER) cc_final: 0.6306 (m100) REVERT: F 170 LYS cc_start: 0.8116 (tttt) cc_final: 0.7885 (tttt) REVERT: F 179 LYS cc_start: 0.7407 (mmtt) cc_final: 0.7119 (mttt) REVERT: F 191 HIS cc_start: 0.5563 (m-70) cc_final: 0.4961 (m-70) REVERT: F 210 PHE cc_start: 0.6404 (t80) cc_final: 0.6049 (t80) REVERT: F 231 ARG cc_start: 0.7659 (ttt-90) cc_final: 0.7437 (ttt-90) REVERT: H 52 VAL cc_start: 0.7603 (t) cc_final: 0.7403 (t) REVERT: H 59 MET cc_start: 0.7055 (tmm) cc_final: 0.6574 (tmm) REVERT: H 103 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6358 (mm-30) REVERT: H 131 LYS cc_start: 0.7262 (tttt) cc_final: 0.6882 (tttt) REVERT: H 153 LYS cc_start: 0.7669 (ptpp) cc_final: 0.7463 (pttm) REVERT: J 163 PHE cc_start: 0.5802 (t80) cc_final: 0.5530 (t80) REVERT: L 29 ILE cc_start: 0.4950 (OUTLIER) cc_final: 0.4491 (tp) REVERT: L 81 GLU cc_start: 0.7182 (pt0) cc_final: 0.6418 (pm20) REVERT: L 97 THR cc_start: 0.7163 (m) cc_final: 0.6899 (p) outliers start: 62 outliers final: 44 residues processed: 474 average time/residue: 0.1557 time to fit residues: 113.0858 Evaluate side-chains 478 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 428 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 14 TRP Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 116 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.224629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.189036 restraints weight = 34249.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.194655 restraints weight = 17980.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.198153 restraints weight = 10850.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.200401 restraints weight = 7385.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.201796 restraints weight = 5525.134| |-----------------------------------------------------------------------------| r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22128 Z= 0.140 Angle : 0.621 10.369 30051 Z= 0.318 Chirality : 0.045 0.202 3315 Planarity : 0.004 0.049 3864 Dihedral : 4.305 39.022 3005 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.36 % Allowed : 14.45 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2757 helix: -0.46 (0.29), residues: 288 sheet: 0.49 (0.19), residues: 750 loop : -0.64 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 61 TYR 0.029 0.002 TYR A 108 PHE 0.029 0.002 PHE F 154 TRP 0.036 0.002 TRP F 70 HIS 0.008 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00310 (22098) covalent geometry : angle 0.61806 (29991) SS BOND : bond 0.00268 ( 30) SS BOND : angle 1.38838 ( 60) hydrogen bonds : bond 0.04137 ( 676) hydrogen bonds : angle 5.64319 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 440 time to evaluate : 0.737 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: A 170 LYS cc_start: 0.7666 (tttt) cc_final: 0.7362 (ttmm) REVERT: A 171 LEU cc_start: 0.7446 (mt) cc_final: 0.7164 (tp) REVERT: A 175 TYR cc_start: 0.6847 (t80) cc_final: 0.6560 (t80) REVERT: A 293 LYS cc_start: 0.7091 (mttt) cc_final: 0.6669 (mttt) REVERT: A 312 LYS cc_start: 0.7283 (mttt) cc_final: 0.6801 (mptt) REVERT: A 318 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7082 (ttmt) REVERT: A 319 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 74 GLU cc_start: 0.5341 (mp0) cc_final: 0.5108 (mp0) REVERT: B 110 TYR cc_start: 0.7053 (t80) cc_final: 0.6694 (t80) REVERT: B 131 LYS cc_start: 0.7416 (tttt) cc_final: 0.7000 (tttt) REVERT: C 36 TRP cc_start: 0.5970 (m100) cc_final: 0.5227 (m100) REVERT: C 67 ARG cc_start: 0.7026 (mtm180) cc_final: 0.6717 (mtm180) REVERT: C 70 ILE cc_start: 0.4732 (OUTLIER) cc_final: 0.4392 (tp) REVERT: C 122 GLN cc_start: 0.6072 (mm-40) cc_final: 0.5835 (mm-40) REVERT: D 81 GLU cc_start: 0.6929 (pm20) cc_final: 0.6558 (pm20) REVERT: D 82 ASP cc_start: 0.7186 (m-30) cc_final: 0.6123 (m-30) REVERT: E 170 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7781 (ttpp) REVERT: E 231 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7429 (mtp-110) REVERT: E 267 MET cc_start: 0.6703 (ppp) cc_final: 0.5701 (ppp) REVERT: E 276 ILE cc_start: 0.5154 (OUTLIER) cc_final: 0.4918 (mt) REVERT: E 278 SER cc_start: 0.6970 (OUTLIER) cc_final: 0.6614 (p) REVERT: E 315 LYS cc_start: 0.4489 (mttt) cc_final: 0.2992 (mttt) REVERT: E 323 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.7342 (mmm160) REVERT: G 17 MET cc_start: 0.6597 (ttp) cc_final: 0.6254 (ttp) REVERT: G 60 ASN cc_start: 0.7715 (p0) cc_final: 0.7340 (p0) REVERT: G 95 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7953 (t0) REVERT: G 103 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6939 (mm-30) REVERT: G 121 LYS cc_start: 0.7984 (tttt) cc_final: 0.7701 (tmtt) REVERT: G 149 MET cc_start: 0.5828 (mmm) cc_final: 0.5391 (mmm) REVERT: G 158 ASP cc_start: 0.7050 (t0) cc_final: 0.6709 (t0) REVERT: I 29 PHE cc_start: 0.6769 (t80) cc_final: 0.6510 (t80) REVERT: I 36 TRP cc_start: 0.4962 (m100) cc_final: 0.4613 (m100) REVERT: K 6 GLN cc_start: 0.6108 (mp10) cc_final: 0.5726 (mp10) REVERT: K 36 TYR cc_start: 0.4957 (m-80) cc_final: 0.4108 (m-80) REVERT: K 61 ARG cc_start: 0.7661 (mtm110) cc_final: 0.7105 (ttp-110) REVERT: K 82 ASP cc_start: 0.6919 (m-30) cc_final: 0.6243 (m-30) REVERT: F 70 TRP cc_start: 0.6561 (t60) cc_final: 0.5950 (t60) REVERT: F 123 ARG cc_start: 0.7303 (ttp80) cc_final: 0.7076 (ttp80) REVERT: F 133 TRP cc_start: 0.6428 (m-90) cc_final: 0.6120 (m-90) REVERT: F 160 TRP cc_start: 0.6532 (OUTLIER) cc_final: 0.6300 (m100) REVERT: F 170 LYS cc_start: 0.8132 (tttt) cc_final: 0.7899 (tttt) REVERT: F 179 LYS cc_start: 0.7412 (mmtt) cc_final: 0.7084 (mttt) REVERT: F 191 HIS cc_start: 0.5514 (m-70) cc_final: 0.4933 (m-70) REVERT: F 210 PHE cc_start: 0.6373 (t80) cc_final: 0.6029 (t80) REVERT: F 231 ARG cc_start: 0.7720 (ttt-90) cc_final: 0.7440 (ttt-90) REVERT: F 318 LYS cc_start: 0.7494 (mtmt) cc_final: 0.7227 (mmmm) REVERT: F 319 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8187 (p) REVERT: H 52 VAL cc_start: 0.7626 (t) cc_final: 0.7397 (t) REVERT: H 59 MET cc_start: 0.7066 (tmm) cc_final: 0.6565 (tmm) REVERT: H 103 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6402 (mm-30) REVERT: H 131 LYS cc_start: 0.7274 (tttt) cc_final: 0.6880 (tttt) REVERT: H 153 LYS cc_start: 0.7730 (ptpp) cc_final: 0.7461 (pttm) REVERT: J 163 PHE cc_start: 0.5776 (t80) cc_final: 0.5542 (t80) REVERT: L 29 ILE cc_start: 0.4921 (OUTLIER) cc_final: 0.4557 (tp) REVERT: L 81 GLU cc_start: 0.7204 (pt0) cc_final: 0.6413 (pm20) REVERT: L 97 THR cc_start: 0.7120 (m) cc_final: 0.6901 (p) outliers start: 57 outliers final: 37 residues processed: 472 average time/residue: 0.1565 time to fit residues: 112.2655 Evaluate side-chains 478 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 432 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 14 TRP Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 150 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 139 optimal weight: 0.0870 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.217419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.182189 restraints weight = 33816.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.187753 restraints weight = 17698.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.191178 restraints weight = 10686.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.193390 restraints weight = 7212.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.194711 restraints weight = 5350.191| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22128 Z= 0.251 Angle : 0.725 11.463 30051 Z= 0.378 Chirality : 0.048 0.226 3315 Planarity : 0.005 0.051 3864 Dihedral : 4.869 42.198 3005 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.57 % Allowed : 14.16 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2757 helix: -0.82 (0.28), residues: 288 sheet: 0.09 (0.18), residues: 843 loop : -0.81 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 61 TYR 0.043 0.002 TYR F 17 PHE 0.041 0.002 PHE F 154 TRP 0.032 0.003 TRP F 70 HIS 0.009 0.002 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00536 (22098) covalent geometry : angle 0.72138 (29991) SS BOND : bond 0.00399 ( 30) SS BOND : angle 1.78632 ( 60) hydrogen bonds : bond 0.05104 ( 676) hydrogen bonds : angle 6.00285 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 454 time to evaluate : 0.825 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: A 170 LYS cc_start: 0.7824 (tttt) cc_final: 0.7492 (mmtt) REVERT: A 171 LEU cc_start: 0.7679 (mt) cc_final: 0.7338 (tp) REVERT: A 175 TYR cc_start: 0.6785 (t80) cc_final: 0.6515 (t80) REVERT: A 177 ASN cc_start: 0.7673 (t0) cc_final: 0.6865 (t0) REVERT: A 217 SER cc_start: 0.7648 (m) cc_final: 0.7208 (p) REVERT: A 293 LYS cc_start: 0.7456 (mttt) cc_final: 0.6996 (mttt) REVERT: A 305 ILE cc_start: 0.8130 (mt) cc_final: 0.7758 (mm) REVERT: A 312 LYS cc_start: 0.7481 (mttt) cc_final: 0.6956 (mptt) REVERT: A 318 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7654 (ttmt) REVERT: A 319 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 74 GLU cc_start: 0.5372 (mp0) cc_final: 0.5110 (mp0) REVERT: B 110 TYR cc_start: 0.7095 (t80) cc_final: 0.6782 (t80) REVERT: B 131 LYS cc_start: 0.7481 (tttt) cc_final: 0.7188 (tttt) REVERT: B 149 MET cc_start: 0.6041 (mmm) cc_final: 0.5745 (mmp) REVERT: C 36 TRP cc_start: 0.6027 (m100) cc_final: 0.5035 (m100) REVERT: C 70 ILE cc_start: 0.4859 (OUTLIER) cc_final: 0.4490 (tp) REVERT: C 122 GLN cc_start: 0.5931 (mm-40) cc_final: 0.5698 (mm-40) REVERT: D 81 GLU cc_start: 0.7001 (pm20) cc_final: 0.6699 (pm20) REVERT: E 121 PHE cc_start: 0.6397 (t80) cc_final: 0.5855 (t80) REVERT: E 164 LYS cc_start: 0.4782 (mtpt) cc_final: 0.4404 (mtpt) REVERT: E 170 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7775 (ttpp) REVERT: E 231 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7409 (mtp-110) REVERT: E 233 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6909 (mm-40) REVERT: E 267 MET cc_start: 0.6662 (ppp) cc_final: 0.5707 (ppp) REVERT: E 312 LYS cc_start: 0.7292 (mttt) cc_final: 0.7052 (mttt) REVERT: E 315 LYS cc_start: 0.4565 (mttt) cc_final: 0.3061 (mttt) REVERT: E 323 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7383 (mtp85) REVERT: G 17 MET cc_start: 0.6719 (ttp) cc_final: 0.6372 (ttp) REVERT: G 60 ASN cc_start: 0.7859 (p0) cc_final: 0.7484 (p0) REVERT: G 103 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7055 (mm-30) REVERT: G 121 LYS cc_start: 0.8053 (tttt) cc_final: 0.7703 (tmtt) REVERT: G 149 MET cc_start: 0.6206 (mmm) cc_final: 0.5791 (mmm) REVERT: G 158 ASP cc_start: 0.7284 (t0) cc_final: 0.6914 (t0) REVERT: I 29 PHE cc_start: 0.6969 (t80) cc_final: 0.6479 (t80) REVERT: I 36 TRP cc_start: 0.5066 (m100) cc_final: 0.4748 (m100) REVERT: I 112 TYR cc_start: 0.5729 (m-10) cc_final: 0.5370 (m-10) REVERT: K 61 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7274 (ttp-110) REVERT: K 82 ASP cc_start: 0.7175 (m-30) cc_final: 0.6460 (m-30) REVERT: F 160 TRP cc_start: 0.6669 (OUTLIER) cc_final: 0.6421 (m100) REVERT: F 170 LYS cc_start: 0.8215 (tttt) cc_final: 0.8007 (tttt) REVERT: F 179 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7153 (mttp) REVERT: F 191 HIS cc_start: 0.5397 (m-70) cc_final: 0.4847 (m-70) REVERT: F 318 LYS cc_start: 0.7516 (mtmt) cc_final: 0.7307 (mmmm) REVERT: F 319 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8287 (p) REVERT: F 321 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7520 (ttmt) REVERT: H 51 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7465 (ttmt) REVERT: H 59 MET cc_start: 0.7116 (tmm) cc_final: 0.6677 (tmm) REVERT: H 103 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6473 (mm-30) REVERT: H 131 LYS cc_start: 0.7335 (tttt) cc_final: 0.6944 (tttt) REVERT: H 153 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7693 (pttp) REVERT: L 29 ILE cc_start: 0.4830 (OUTLIER) cc_final: 0.4464 (tp) REVERT: L 37 GLN cc_start: 0.7608 (tt0) cc_final: 0.7308 (tt0) REVERT: L 72 THR cc_start: 0.7724 (m) cc_final: 0.7403 (t) REVERT: L 81 GLU cc_start: 0.7287 (pt0) cc_final: 0.6432 (pm20) REVERT: L 82 ASP cc_start: 0.7125 (m-30) cc_final: 0.4766 (m-30) outliers start: 62 outliers final: 45 residues processed: 486 average time/residue: 0.1479 time to fit residues: 110.9193 Evaluate side-chains 494 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 443 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 92 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 272 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.220753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.185709 restraints weight = 33831.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.191324 restraints weight = 17478.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.194799 restraints weight = 10540.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.196968 restraints weight = 7089.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.198284 restraints weight = 5229.800| |-----------------------------------------------------------------------------| r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22128 Z= 0.156 Angle : 0.659 10.489 30051 Z= 0.339 Chirality : 0.046 0.325 3315 Planarity : 0.004 0.052 3864 Dihedral : 4.647 40.897 3005 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.78 % Allowed : 15.57 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2757 helix: -0.92 (0.28), residues: 306 sheet: 0.45 (0.19), residues: 774 loop : -0.76 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 61 TYR 0.031 0.002 TYR F 17 PHE 0.038 0.002 PHE F 154 TRP 0.051 0.002 TRP H 92 HIS 0.008 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00347 (22098) covalent geometry : angle 0.65644 (29991) SS BOND : bond 0.00321 ( 30) SS BOND : angle 1.47861 ( 60) hydrogen bonds : bond 0.04339 ( 676) hydrogen bonds : angle 5.76787 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 446 time to evaluate : 0.810 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: A 170 LYS cc_start: 0.7596 (tttt) cc_final: 0.7274 (mmtt) REVERT: A 171 LEU cc_start: 0.7508 (mt) cc_final: 0.7200 (tp) REVERT: A 175 TYR cc_start: 0.6757 (t80) cc_final: 0.6457 (t80) REVERT: A 231 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7169 (ttt-90) REVERT: A 293 LYS cc_start: 0.7252 (mttt) cc_final: 0.6829 (mttt) REVERT: A 305 ILE cc_start: 0.8096 (mt) cc_final: 0.7788 (mm) REVERT: A 312 LYS cc_start: 0.7295 (mttt) cc_final: 0.6809 (mptt) REVERT: A 318 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7502 (ttmt) REVERT: A 319 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8268 (p) REVERT: B 74 GLU cc_start: 0.5449 (mp0) cc_final: 0.5181 (mp0) REVERT: B 110 TYR cc_start: 0.7042 (t80) cc_final: 0.6735 (t80) REVERT: B 131 LYS cc_start: 0.7466 (tttt) cc_final: 0.7115 (tttt) REVERT: C 36 TRP cc_start: 0.6006 (m100) cc_final: 0.5182 (m100) REVERT: C 70 ILE cc_start: 0.4809 (OUTLIER) cc_final: 0.4449 (tp) REVERT: C 122 GLN cc_start: 0.5948 (mm-40) cc_final: 0.5713 (mm-40) REVERT: D 81 GLU cc_start: 0.6946 (pm20) cc_final: 0.6551 (pm20) REVERT: D 82 ASP cc_start: 0.7343 (m-30) cc_final: 0.6046 (m-30) REVERT: E 121 PHE cc_start: 0.6311 (t80) cc_final: 0.5794 (t80) REVERT: E 170 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7786 (ttpp) REVERT: E 176 ILE cc_start: 0.7770 (mt) cc_final: 0.7498 (mp) REVERT: E 231 ARG cc_start: 0.8184 (mtt-85) cc_final: 0.7459 (mtp-110) REVERT: E 233 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6857 (mm-40) REVERT: E 237 MET cc_start: 0.5093 (tpp) cc_final: 0.4777 (tpp) REVERT: E 267 MET cc_start: 0.6680 (ppp) cc_final: 0.5694 (ppp) REVERT: E 315 LYS cc_start: 0.4618 (mttt) cc_final: 0.3235 (mttt) REVERT: G 17 MET cc_start: 0.6607 (ttp) cc_final: 0.6241 (ttp) REVERT: G 46 ASP cc_start: 0.6561 (m-30) cc_final: 0.6128 (m-30) REVERT: G 48 ILE cc_start: 0.8368 (mm) cc_final: 0.8061 (mm) REVERT: G 60 ASN cc_start: 0.7832 (p0) cc_final: 0.7480 (p0) REVERT: G 103 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6981 (mm-30) REVERT: G 121 LYS cc_start: 0.7965 (tttt) cc_final: 0.7659 (tmtt) REVERT: G 149 MET cc_start: 0.6041 (mmm) cc_final: 0.5623 (mmm) REVERT: G 158 ASP cc_start: 0.7221 (t0) cc_final: 0.6831 (t0) REVERT: I 29 PHE cc_start: 0.6877 (t80) cc_final: 0.6648 (t80) REVERT: I 36 TRP cc_start: 0.5000 (m100) cc_final: 0.4750 (m100) REVERT: K 61 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7221 (ttp-110) REVERT: K 82 ASP cc_start: 0.7158 (m-30) cc_final: 0.6457 (m-30) REVERT: F 70 TRP cc_start: 0.6502 (t60) cc_final: 0.6137 (t60) REVERT: F 160 TRP cc_start: 0.6555 (OUTLIER) cc_final: 0.6328 (m100) REVERT: F 179 LYS cc_start: 0.7430 (mmtt) cc_final: 0.7135 (mttt) REVERT: F 191 HIS cc_start: 0.5540 (m-70) cc_final: 0.5006 (m-70) REVERT: F 319 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8244 (p) REVERT: F 321 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7545 (ttmt) REVERT: H 59 MET cc_start: 0.7083 (tmm) cc_final: 0.6669 (tmm) REVERT: H 103 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6379 (mm-30) REVERT: H 131 LYS cc_start: 0.7359 (tttt) cc_final: 0.6934 (tttt) REVERT: H 153 LYS cc_start: 0.7891 (ptpp) cc_final: 0.7603 (pttm) REVERT: L 37 GLN cc_start: 0.7724 (tt0) cc_final: 0.7445 (tt0) REVERT: L 72 THR cc_start: 0.7714 (m) cc_final: 0.7393 (t) REVERT: L 81 GLU cc_start: 0.7245 (pt0) cc_final: 0.6418 (pm20) REVERT: L 82 ASP cc_start: 0.7037 (m-30) cc_final: 0.5435 (m-30) outliers start: 43 outliers final: 35 residues processed: 472 average time/residue: 0.1556 time to fit residues: 112.4750 Evaluate side-chains 480 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 440 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 14 TRP Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 100 optimal weight: 0.0030 chunk 249 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 187 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.220778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.185527 restraints weight = 33984.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.191205 restraints weight = 17821.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.194602 restraints weight = 10705.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.196847 restraints weight = 7253.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.198305 restraints weight = 5357.131| |-----------------------------------------------------------------------------| r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5694 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22128 Z= 0.151 Angle : 0.650 10.303 30051 Z= 0.334 Chirality : 0.045 0.197 3315 Planarity : 0.004 0.050 3864 Dihedral : 4.593 40.354 3005 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.78 % Allowed : 16.19 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2757 helix: -0.89 (0.28), residues: 306 sheet: 0.52 (0.19), residues: 771 loop : -0.75 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 61 TYR 0.031 0.002 TYR F 17 PHE 0.036 0.002 PHE F 154 TRP 0.050 0.002 TRP H 92 HIS 0.008 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00336 (22098) covalent geometry : angle 0.64711 (29991) SS BOND : bond 0.00301 ( 30) SS BOND : angle 1.58334 ( 60) hydrogen bonds : bond 0.04274 ( 676) hydrogen bonds : angle 5.68404 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5252.57 seconds wall clock time: 90 minutes 54.26 seconds (5454.26 seconds total)