Starting phenix.real_space_refine on Wed Jan 15 00:15:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d9l_46676/01_2025/9d9l_46676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d9l_46676/01_2025/9d9l_46676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d9l_46676/01_2025/9d9l_46676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d9l_46676/01_2025/9d9l_46676.map" model { file = "/net/cci-nas-00/data/ceres_data/9d9l_46676/01_2025/9d9l_46676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d9l_46676/01_2025/9d9l_46676.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 C 16140 2.51 5 N 4128 2.21 5 O 5220 1.98 5 H 24441 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 49929 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4161 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "B" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4161 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "C" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4160 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "D" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4161 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "E" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4163 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "F" Number of atoms: 4162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4162 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "G" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4160 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "H" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4160 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "I" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4160 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "J" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4160 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "K" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4161 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain: "L" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4160 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 272} Time building chain proxies: 18.79, per 1000 atoms: 0.38 Number of scatterers: 49929 At special positions: 0 Unit cell: (181.2, 165.6, 141.6, 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) O 5220 8.00 N 4128 7.00 C 16140 6.00 H 24441 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.68 Conformation dependent library (CDL) restraints added in 3.2 seconds 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 65 sheets defined 11.4% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.607A pdb=" N VAL A 8 " --> pdb=" O ASP A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 99 through 108 removed outlier: 4.807A pdb=" N LEU A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.874A pdb=" N LYS B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 4.867A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.659A pdb=" N ALA C 7 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 8 " --> pdb=" O ASP C 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4 through 8' Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 99 through 108 removed outlier: 4.864A pdb=" N LEU C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'D' and resid 4 through 8 removed outlier: 3.698A pdb=" N ALA D 7 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 8 " --> pdb=" O ASP D 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4 through 8' Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.816A pdb=" N LYS D 32 " --> pdb=" O PRO D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 107 removed outlier: 4.849A pdb=" N LEU D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.618A pdb=" N ILE D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.905A pdb=" N LYS E 32 " --> pdb=" O PRO E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 107 removed outlier: 4.966A pdb=" N LEU E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'F' and resid 27 through 32 removed outlier: 3.825A pdb=" N LYS F 32 " --> pdb=" O PRO F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 107 removed outlier: 3.521A pdb=" N GLU F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'G' and resid 99 through 107 removed outlier: 4.414A pdb=" N LEU G 105 " --> pdb=" O THR G 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 238 Processing helix chain 'G' and resid 244 through 248 Processing helix chain 'H' and resid 4 through 8 removed outlier: 3.502A pdb=" N ALA H 7 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL H 8 " --> pdb=" O ASP H 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 4 through 8' Processing helix chain 'H' and resid 27 through 32 removed outlier: 4.225A pdb=" N LYS H 32 " --> pdb=" O PRO H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 42 removed outlier: 4.055A pdb=" N TRP H 42 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 108 removed outlier: 4.361A pdb=" N LEU H 105 " --> pdb=" O THR H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 237 Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.624A pdb=" N LYS I 32 " --> pdb=" O SER I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 42 removed outlier: 3.589A pdb=" N TRP I 42 " --> pdb=" O PRO I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 108 removed outlier: 4.865A pdb=" N LEU I 105 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR I 106 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 235 Processing helix chain 'I' and resid 244 through 248 removed outlier: 3.629A pdb=" N TRP I 248 " --> pdb=" O GLU I 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 8 removed outlier: 3.612A pdb=" N VAL J 8 " --> pdb=" O ASP J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 32 removed outlier: 3.991A pdb=" N LYS J 32 " --> pdb=" O PRO J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 42 Processing helix chain 'J' and resid 99 through 107 removed outlier: 4.768A pdb=" N LEU J 105 " --> pdb=" O THR J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 235 Processing helix chain 'J' and resid 237 through 241 Processing helix chain 'J' and resid 244 through 248 Processing helix chain 'K' and resid 29 through 33 Processing helix chain 'K' and resid 99 through 107 removed outlier: 4.777A pdb=" N LEU K 105 " --> pdb=" O THR K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 218 Processing helix chain 'K' and resid 228 through 238 Processing helix chain 'K' and resid 244 through 248 removed outlier: 3.519A pdb=" N TRP K 248 " --> pdb=" O GLU K 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 8 removed outlier: 3.749A pdb=" N ALA L 7 " --> pdb=" O LYS L 4 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL L 8 " --> pdb=" O ASP L 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 4 through 8' Processing helix chain 'L' and resid 27 through 32 removed outlier: 3.871A pdb=" N LYS L 32 " --> pdb=" O PRO L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 42 removed outlier: 3.683A pdb=" N TRP L 42 " --> pdb=" O PRO L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 108 removed outlier: 4.966A pdb=" N LEU L 105 " --> pdb=" O THR L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 248 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.453A pdb=" N ARG A 129 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS A 148 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP A 89 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.453A pdb=" N ARG A 129 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS A 148 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 182 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.725A pdb=" N TYR B 182 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 148 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 129 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.725A pdb=" N TYR B 182 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 95 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP B 89 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 252 Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA8, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA9, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AB1, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.705A pdb=" N TYR C 182 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS C 148 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG C 129 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG C 13 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.705A pdb=" N TYR C 182 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP C 89 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 249 through 252 Processing sheet with id=AB4, first strand: chain 'B' and resid 218 through 223 removed outlier: 5.018A pdb=" N SER B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 215 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLY B 221 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 213 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR B 212 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AB6, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.663A pdb=" N TYR D 182 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS D 148 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG D 129 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA D 19 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.663A pdb=" N TYR D 182 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASP D 89 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 249 through 253 Processing sheet with id=AB9, first strand: chain 'C' and resid 218 through 219 Processing sheet with id=AC1, first strand: chain 'C' and resid 218 through 219 removed outlier: 7.170A pdb=" N ASP C 210 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASP C 270 " --> pdb=" O ASP C 210 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR C 212 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 68 through 70 Processing sheet with id=AC3, first strand: chain 'D' and resid 117 through 120 removed outlier: 3.749A pdb=" N TYR E 182 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS E 148 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG E 129 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 117 through 120 removed outlier: 3.749A pdb=" N TYR E 182 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS E 148 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 95 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP E 89 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP E 64 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 249 through 253 Processing sheet with id=AC6, first strand: chain 'D' and resid 218 through 224 removed outlier: 5.288A pdb=" N SER D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 215 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY D 221 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU D 213 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE D 223 " --> pdb=" O TYR D 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 218 through 224 removed outlier: 5.288A pdb=" N SER D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 215 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLY D 221 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU D 213 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE D 223 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP D 210 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 67 through 73 removed outlier: 6.830A pdb=" N ASP E 67 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER E 73 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS E 78 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.614A pdb=" N TYR F 182 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS F 148 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG F 129 " --> pdb=" O LYS F 148 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.614A pdb=" N TYR F 182 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU F 95 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP F 89 " --> pdb=" O PHE F 173 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 249 through 253 removed outlier: 4.511A pdb=" N VAL E 198 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 218 through 224 removed outlier: 3.521A pdb=" N LEU E 213 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP E 222 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR E 211 " --> pdb=" O ASP E 222 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP E 210 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP E 270 " --> pdb=" O ASP E 210 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR E 212 " --> pdb=" O GLY E 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 67 through 73 removed outlier: 6.758A pdb=" N ASP F 67 " --> pdb=" O THR F 84 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER F 73 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LYS F 78 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 218 through 219 Processing sheet with id=AD6, first strand: chain 'F' and resid 249 through 250 Processing sheet with id=AD7, first strand: chain 'G' and resid 48 through 49 removed outlier: 6.514A pdb=" N ARG G 129 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS G 148 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP G 89 " --> pdb=" O PHE G 173 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 48 through 49 removed outlier: 6.514A pdb=" N ARG G 129 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS G 148 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR G 182 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 68 through 70 Processing sheet with id=AE1, first strand: chain 'G' and resid 117 through 120 removed outlier: 3.559A pdb=" N TYR H 182 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS H 148 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG H 129 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 117 through 120 removed outlier: 3.559A pdb=" N TYR H 182 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR H 172 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP H 89 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 249 through 253 removed outlier: 3.553A pdb=" N ASP G 253 " --> pdb=" O ASP G 256 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 218 through 219 Processing sheet with id=AE5, first strand: chain 'G' and resid 218 through 219 removed outlier: 4.063A pdb=" N VAL G 269 " --> pdb=" O THR G 212 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU G 214 " --> pdb=" O LEU G 267 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU G 267 " --> pdb=" O LEU G 214 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 68 through 71 Processing sheet with id=AE7, first strand: chain 'H' and resid 117 through 120 removed outlier: 3.981A pdb=" N TYR I 182 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS I 148 " --> pdb=" O ARG I 129 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG I 129 " --> pdb=" O LYS I 148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 117 through 120 removed outlier: 3.981A pdb=" N TYR I 182 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP I 89 " --> pdb=" O PHE I 173 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 249 through 253 Processing sheet with id=AF1, first strand: chain 'H' and resid 218 through 219 Processing sheet with id=AF2, first strand: chain 'I' and resid 68 through 71 Processing sheet with id=AF3, first strand: chain 'I' and resid 117 through 120 removed outlier: 3.873A pdb=" N TYR J 182 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS J 148 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG J 129 " --> pdb=" O LYS J 148 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 117 through 120 removed outlier: 3.873A pdb=" N TYR J 182 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR J 172 " --> pdb=" O SER J 150 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP J 89 " --> pdb=" O PHE J 173 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 249 through 252 Processing sheet with id=AF6, first strand: chain 'I' and resid 218 through 219 Processing sheet with id=AF7, first strand: chain 'I' and resid 218 through 219 removed outlier: 6.762A pdb=" N ASP I 210 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP I 270 " --> pdb=" O ASP I 210 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR I 212 " --> pdb=" O GLY I 268 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 68 through 73 removed outlier: 7.460A pdb=" N SER J 73 " --> pdb=" O LYS J 78 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS J 78 " --> pdb=" O SER J 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 117 through 120 removed outlier: 4.060A pdb=" N TYR K 182 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS K 148 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG K 129 " --> pdb=" O LYS K 148 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 117 through 120 removed outlier: 4.060A pdb=" N TYR K 182 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 95 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP K 89 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 249 through 253 Processing sheet with id=AG3, first strand: chain 'J' and resid 218 through 219 removed outlier: 6.523A pdb=" N THR J 212 " --> pdb=" O GLY J 268 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 67 through 73 removed outlier: 6.612A pdb=" N ASP K 67 " --> pdb=" O THR K 84 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER K 73 " --> pdb=" O LYS K 78 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS K 78 " --> pdb=" O SER K 73 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 117 through 120 removed outlier: 4.109A pdb=" N TYR L 182 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS L 148 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG L 129 " --> pdb=" O LYS L 148 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 117 through 120 removed outlier: 4.109A pdb=" N TYR L 182 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP L 89 " --> pdb=" O PHE L 173 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 249 through 250 Processing sheet with id=AG8, first strand: chain 'K' and resid 223 through 224 removed outlier: 6.952A pdb=" N ASP K 210 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP K 270 " --> pdb=" O ASP K 210 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR K 212 " --> pdb=" O GLY K 268 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 68 through 71 Processing sheet with id=AH1, first strand: chain 'L' and resid 249 through 253 Processing sheet with id=AH2, first strand: chain 'L' and resid 218 through 219 removed outlier: 4.681A pdb=" N LEU L 214 " --> pdb=" O ALA L 266 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2298 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: 16.74 Time building geometry restraints manager: 11.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.07: 5169 1.07 - 1.20: 19272 1.20 - 1.32: 5238 1.32 - 1.45: 6205 1.45 - 1.58: 14561 Bond restraints: 50445 Sorted by residual: bond pdb=" NE2 HIS F 145 " pdb=" HE2 HIS F 145 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CZ3 TRP F 42 " pdb=" HZ3 TRP F 42 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU A 263 " pdb=" H LEU A 263 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD1 TYR I 199 " pdb=" HD1 TYR I 199 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE1 TRP F 42 " pdb=" HE1 TRP F 42 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 50440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.81: 90301 6.81 - 13.61: 722 13.61 - 20.42: 0 20.42 - 27.22: 0 27.22 - 34.03: 3 Bond angle restraints: 91026 Sorted by residual: angle pdb=" N ILE D 236 " pdb=" CA ILE D 236 " pdb=" HA ILE D 236 " ideal model delta sigma weight residual 110.00 75.97 34.03 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C ILE D 236 " pdb=" CA ILE D 236 " pdb=" HA ILE D 236 " ideal model delta sigma weight residual 109.00 76.72 32.28 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CB ILE D 236 " pdb=" CA ILE D 236 " pdb=" HA ILE D 236 " ideal model delta sigma weight residual 109.00 78.40 30.60 3.00e+00 1.11e-01 1.04e+02 angle pdb=" CA ASP G 35 " pdb=" CB ASP G 35 " pdb=" CG ASP G 35 " ideal model delta sigma weight residual 112.60 119.60 -7.00 1.00e+00 1.00e+00 4.90e+01 angle pdb=" CA ASP B 256 " pdb=" CB ASP B 256 " pdb=" CG ASP B 256 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.00e+00 1.00e+00 4.08e+01 ... (remaining 91021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 21489 17.62 - 35.24: 1429 35.24 - 52.86: 504 52.86 - 70.48: 353 70.48 - 88.10: 18 Dihedral angle restraints: 23793 sinusoidal: 12600 harmonic: 11193 Sorted by residual: dihedral pdb=" C ILE D 236 " pdb=" N ILE D 236 " pdb=" CA ILE D 236 " pdb=" CB ILE D 236 " ideal model delta harmonic sigma weight residual -122.00 -137.51 15.51 0 2.50e+00 1.60e-01 3.85e+01 dihedral pdb=" CA TRP B 42 " pdb=" C TRP B 42 " pdb=" N ASP B 43 " pdb=" CA ASP B 43 " ideal model delta harmonic sigma weight residual 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA TYR K 176 " pdb=" C TYR K 176 " pdb=" N GLN K 177 " pdb=" CA GLN K 177 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 23790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2959 0.104 - 0.208: 981 0.208 - 0.312: 106 0.312 - 0.417: 27 0.417 - 0.521: 7 Chirality restraints: 4080 Sorted by residual: chirality pdb=" CA ASP D 139 " pdb=" N ASP D 139 " pdb=" C ASP D 139 " pdb=" CB ASP D 139 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" CA ASP A 139 " pdb=" N ASP A 139 " pdb=" C ASP A 139 " pdb=" CB ASP A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA ASP C 139 " pdb=" N ASP C 139 " pdb=" C ASP C 139 " pdb=" CB ASP C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 ... (remaining 4077 not shown) Planarity restraints: 7920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 184 " 0.177 2.00e-02 2.50e+03 8.09e-02 2.62e+02 pdb=" CG TRP H 184 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP H 184 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP H 184 " -0.068 2.00e-02 2.50e+03 pdb=" NE1 TRP H 184 " -0.095 2.00e-02 2.50e+03 pdb=" CE2 TRP H 184 " -0.065 2.00e-02 2.50e+03 pdb=" CE3 TRP H 184 " -0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 184 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 184 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP H 184 " 0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP H 184 " 0.108 2.00e-02 2.50e+03 pdb=" HE1 TRP H 184 " -0.082 2.00e-02 2.50e+03 pdb=" HE3 TRP H 184 " -0.089 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 184 " 0.046 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 184 " -0.022 2.00e-02 2.50e+03 pdb=" HH2 TRP H 184 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 141 " -0.480 9.50e-02 1.11e+02 1.76e-01 1.50e+02 pdb=" NE ARG J 141 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG J 141 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG J 141 " -0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG J 141 " 0.028 2.00e-02 2.50e+03 pdb="HH11 ARG J 141 " -0.111 2.00e-02 2.50e+03 pdb="HH12 ARG J 141 " 0.169 2.00e-02 2.50e+03 pdb="HH21 ARG J 141 " 0.031 2.00e-02 2.50e+03 pdb="HH22 ARG J 141 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 189 " 0.114 2.00e-02 2.50e+03 6.05e-02 1.46e+02 pdb=" CG TRP H 189 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP H 189 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP H 189 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP H 189 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP H 189 " 0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP H 189 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 189 " 0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 189 " -0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP H 189 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 TRP H 189 " -0.086 2.00e-02 2.50e+03 pdb=" HE1 TRP H 189 " -0.080 2.00e-02 2.50e+03 pdb=" HE3 TRP H 189 " -0.026 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 189 " 0.085 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 189 " -0.108 2.00e-02 2.50e+03 pdb=" HH2 TRP H 189 " 0.014 2.00e-02 2.50e+03 ... (remaining 7917 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.16: 2404 2.16 - 2.74: 75488 2.74 - 3.33: 132042 3.33 - 3.91: 170588 3.91 - 4.50: 240991 Nonbonded interactions: 621513 Sorted by model distance: nonbonded pdb=" OD1 ASP C 202 " pdb=" HG SER C 255 " model vdw 1.571 2.450 nonbonded pdb=" OE2 GLU G 86 " pdb=" HG SER L 122 " model vdw 1.575 2.450 nonbonded pdb=" OD2 ASP K 89 " pdb=" HH TYR K 182 " model vdw 1.594 2.450 nonbonded pdb=" HG1 THR G 251 " pdb=" OE1 GLU G 258 " model vdw 1.597 2.450 nonbonded pdb=" OD1 ASP H 210 " pdb=" HG SER H 271 " model vdw 1.599 2.450 ... (remaining 621508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) selection = (chain 'B' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) selection = (chain 'C' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) selection = (chain 'D' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) selection = (chain 'E' and (resid 2 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 39 through 51 or (resid 52 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 53 thro \ ugh 144 or (resid 145 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 146 through 2 \ 83)) selection = (chain 'F' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 144 or (resid 145 and (name N or name CA or name C or name O or name \ CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name \ HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 146 t \ hrough 283)) selection = (chain 'G' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) selection = (chain 'H' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) selection = (chain 'I' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) selection = (chain 'J' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) selection = (chain 'K' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 144 or (resid 145 and (name N or name CA or name C or name O or name \ CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name \ HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 146 t \ hrough 283)) selection = (chain 'L' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 53 through 283)) } 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: 2.070 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: 0.700 Extract box with map and model: 1.510 Check model and map are aligned: 0.270 Set scattering table: 0.360 Process input model: 80.840 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 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 : 0.012 0.042 26004 Z= 0.790 Angle : 1.864 7.951 35520 Z= 1.235 Chirality : 0.099 0.521 4080 Planarity : 0.012 0.151 4656 Dihedral : 13.797 88.097 8964 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.87 % Allowed : 6.70 % Favored : 92.42 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3360 helix: -2.98 (0.25), residues: 208 sheet: -0.59 (0.17), residues: 851 loop : -1.01 (0.11), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.126 0.019 TRP H 184 HIS 0.013 0.003 HIS C 145 PHE 0.056 0.010 PHE F 173 TYR 0.124 0.016 TYR H 182 ARG 0.008 0.001 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 654 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 631 time to evaluate : 2.852 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 SER cc_start: 0.7040 (t) cc_final: 0.6665 (m) REVERT: B 37 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6835 (mp0) REVERT: B 55 GLU cc_start: 0.7015 (pt0) cc_final: 0.6249 (pm20) REVERT: B 60 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6973 (mt-10) REVERT: B 80 ARG cc_start: 0.6621 (ptt180) cc_final: 0.4657 (mtt-85) REVERT: C 69 GLU cc_start: 0.5946 (pt0) cc_final: 0.5730 (pt0) REVERT: C 104 GLU cc_start: 0.7681 (tt0) cc_final: 0.7281 (tt0) REVERT: D 80 ARG cc_start: 0.5839 (ttp80) cc_final: 0.4843 (ptt-90) REVERT: D 101 THR cc_start: 0.6266 (OUTLIER) cc_final: 0.6013 (p) REVERT: D 199 TYR cc_start: 0.8128 (m-80) cc_final: 0.7763 (m-80) REVERT: E 55 GLU cc_start: 0.7238 (tt0) cc_final: 0.6624 (pt0) REVERT: E 77 LYS cc_start: 0.6596 (mptt) cc_final: 0.6016 (tppt) REVERT: E 86 GLU cc_start: 0.7996 (tt0) cc_final: 0.7516 (mm-30) REVERT: E 99 ASP cc_start: 0.6213 (t70) cc_final: 0.5569 (t70) REVERT: E 104 GLU cc_start: 0.6841 (tt0) cc_final: 0.6503 (tt0) REVERT: E 163 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6895 (mt-10) REVERT: E 164 PHE cc_start: 0.8413 (m-80) cc_final: 0.8016 (m-10) REVERT: F 155 ASP cc_start: 0.7510 (t0) cc_final: 0.7191 (t70) REVERT: F 163 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7160 (tp30) REVERT: G 8 VAL cc_start: 0.7971 (t) cc_final: 0.7623 (m) REVERT: G 35 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.5604 (t70) REVERT: G 55 GLU cc_start: 0.6177 (tm-30) cc_final: 0.5861 (mm-30) REVERT: G 182 TYR cc_start: 0.8235 (p90) cc_final: 0.8006 (p90) REVERT: H 5 ASP cc_start: 0.6990 (m-30) cc_final: 0.5704 (t0) REVERT: H 99 ASP cc_start: 0.6409 (t0) cc_final: 0.5936 (t0) REVERT: H 155 ASP cc_start: 0.8363 (t0) cc_final: 0.7778 (m-30) REVERT: H 188 ASP cc_start: 0.6637 (m-30) cc_final: 0.5883 (t70) REVERT: I 13 ARG cc_start: 0.6670 (ttp80) cc_final: 0.6058 (tpt170) REVERT: I 60 GLU cc_start: 0.7635 (tp30) cc_final: 0.7377 (tt0) REVERT: I 67 ASP cc_start: 0.7885 (t0) cc_final: 0.6272 (m-30) REVERT: I 155 ASP cc_start: 0.7522 (t0) cc_final: 0.7046 (m-30) REVERT: I 188 ASP cc_start: 0.7435 (m-30) cc_final: 0.7066 (m-30) REVERT: J 139 ASP cc_start: 0.6969 (p0) cc_final: 0.6690 (p0) REVERT: J 189 TRP cc_start: 0.7345 (m-10) cc_final: 0.6749 (m-10) REVERT: K 40 GLU cc_start: 0.7691 (pm20) cc_final: 0.7489 (mm-30) REVERT: K 70 VAL cc_start: 0.8550 (t) cc_final: 0.8315 (p) REVERT: K 154 GLU cc_start: 0.7507 (tp30) cc_final: 0.7292 (tp30) REVERT: K 155 ASP cc_start: 0.7492 (t0) cc_final: 0.7122 (m-30) REVERT: K 158 SER cc_start: 0.7740 (t) cc_final: 0.7440 (m) REVERT: L 13 ARG cc_start: 0.7062 (ttm170) cc_final: 0.6156 (tpt170) REVERT: L 60 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6590 (mp0) REVERT: L 64 ASP cc_start: 0.6546 (m-30) cc_final: 0.6153 (m-30) REVERT: L 138 ASN cc_start: 0.6949 (t0) cc_final: 0.6745 (t0) REVERT: L 158 SER cc_start: 0.8230 (m) cc_final: 0.7426 (t) outliers start: 23 outliers final: 11 residues processed: 646 average time/residue: 0.7865 time to fit residues: 771.9134 Evaluate side-chains 430 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 417 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 112 SER Chi-restraints excluded: chain L residue 153 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN D 191 ASN E 111 GLN H 191 ASN L 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.152400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.116197 restraints weight = 816743.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.117031 restraints weight = 550390.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.116715 restraints weight = 485352.282| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26004 Z= 0.309 Angle : 0.649 8.925 35520 Z= 0.359 Chirality : 0.048 0.319 4080 Planarity : 0.005 0.060 4656 Dihedral : 7.050 47.750 3635 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 1.63 % Allowed : 11.44 % Favored : 86.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 3360 helix: -1.93 (0.30), residues: 229 sheet: -0.86 (0.15), residues: 1000 loop : -0.79 (0.13), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 189 HIS 0.007 0.001 HIS B 145 PHE 0.018 0.002 PHE E 173 TYR 0.017 0.002 TYR F 211 ARG 0.008 0.001 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 412 time to evaluate : 2.896 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: A 71 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.5533 (ppt170) REVERT: A 154 GLU cc_start: 0.8031 (tp30) cc_final: 0.7806 (tp30) REVERT: B 80 ARG cc_start: 0.7574 (ptt180) cc_final: 0.5991 (mtt-85) REVERT: C 10 ILE cc_start: 0.8110 (mm) cc_final: 0.7714 (mm) REVERT: C 71 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6289 (ptm160) REVERT: C 79 LEU cc_start: 0.8500 (pp) cc_final: 0.8162 (pp) REVERT: D 80 ARG cc_start: 0.7125 (ttp80) cc_final: 0.6061 (ptt-90) REVERT: D 154 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7555 (tm-30) REVERT: E 77 LYS cc_start: 0.6736 (mptt) cc_final: 0.6386 (tppt) REVERT: E 84 THR cc_start: 0.7666 (m) cc_final: 0.7381 (p) REVERT: E 85 GLU cc_start: 0.7828 (tp30) cc_final: 0.7524 (tp30) REVERT: E 214 LEU cc_start: 0.8782 (mt) cc_final: 0.8552 (mp) REVERT: F 78 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7891 (mttm) REVERT: F 175 ASP cc_start: 0.7808 (m-30) cc_final: 0.7518 (m-30) REVERT: F 236 ILE cc_start: 0.8448 (mm) cc_final: 0.8192 (mm) REVERT: G 8 VAL cc_start: 0.8330 (t) cc_final: 0.7901 (m) REVERT: G 172 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7578 (m) REVERT: H 5 ASP cc_start: 0.6665 (m-30) cc_final: 0.5653 (t0) REVERT: H 69 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6699 (mt-10) REVERT: H 99 ASP cc_start: 0.7937 (t0) cc_final: 0.7700 (t0) REVERT: H 138 ASN cc_start: 0.6506 (m110) cc_final: 0.5773 (t0) REVERT: H 155 ASP cc_start: 0.8501 (t0) cc_final: 0.8093 (m-30) REVERT: H 163 GLU cc_start: 0.5349 (mm-30) cc_final: 0.4764 (pt0) REVERT: H 188 ASP cc_start: 0.7611 (m-30) cc_final: 0.6803 (t70) REVERT: I 76 LYS cc_start: 0.8501 (tttt) cc_final: 0.7850 (mtpp) REVERT: I 77 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7707 (tppt) REVERT: I 155 ASP cc_start: 0.7738 (t0) cc_final: 0.7210 (m-30) REVERT: I 188 ASP cc_start: 0.7891 (m-30) cc_final: 0.7603 (m-30) REVERT: I 228 ASN cc_start: 0.7039 (p0) cc_final: 0.6626 (p0) REVERT: J 187 GLU cc_start: 0.6598 (tt0) cc_final: 0.6386 (tp30) REVERT: J 189 TRP cc_start: 0.8203 (m-10) cc_final: 0.7316 (m-10) REVERT: K 47 TRP cc_start: 0.8101 (m100) cc_final: 0.7859 (m100) REVERT: K 154 GLU cc_start: 0.8048 (tp30) cc_final: 0.7435 (tp30) REVERT: K 155 ASP cc_start: 0.8464 (t0) cc_final: 0.8131 (m-30) REVERT: K 176 TYR cc_start: 0.5866 (OUTLIER) cc_final: 0.4029 (t80) REVERT: L 8 VAL cc_start: 0.8523 (t) cc_final: 0.8106 (m) REVERT: L 138 ASN cc_start: 0.6722 (t0) cc_final: 0.6473 (t0) REVERT: L 158 SER cc_start: 0.8376 (m) cc_final: 0.7589 (t) REVERT: L 163 GLU cc_start: 0.6071 (mm-30) cc_final: 0.5224 (mm-30) REVERT: L 246 SER cc_start: 0.8568 (p) cc_final: 0.8202 (p) outliers start: 43 outliers final: 27 residues processed: 446 average time/residue: 0.7716 time to fit residues: 523.9793 Evaluate side-chains 365 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 334 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 176 TYR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 153 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 330 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 chunk 303 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** I 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.146423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.109457 restraints weight = 833344.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.109994 restraints weight = 552122.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.109695 restraints weight = 503275.968| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 26004 Z= 0.517 Angle : 0.705 7.094 35520 Z= 0.387 Chirality : 0.051 0.322 4080 Planarity : 0.005 0.059 4656 Dihedral : 6.662 46.971 3624 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.84 % Allowed : 13.03 % Favored : 84.13 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.13), residues: 3360 helix: -1.78 (0.33), residues: 222 sheet: -1.23 (0.15), residues: 994 loop : -1.17 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 189 HIS 0.008 0.002 HIS B 145 PHE 0.021 0.003 PHE I 257 TYR 0.025 0.002 TYR A 106 ARG 0.006 0.001 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 347 time to evaluate : 2.886 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: A 8 VAL cc_start: 0.8873 (t) cc_final: 0.8631 (m) REVERT: A 49 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7979 (mt) REVERT: A 154 GLU cc_start: 0.8391 (tp30) cc_final: 0.8130 (tp30) REVERT: A 155 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: A 259 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8214 (pt) REVERT: B 32 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8121 (mtpt) REVERT: B 86 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6792 (mm-30) REVERT: C 64 ASP cc_start: 0.8031 (p0) cc_final: 0.7793 (p0) REVERT: C 267 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7912 (mp) REVERT: D 80 ARG cc_start: 0.7203 (ttp80) cc_final: 0.5372 (ptt-90) REVERT: E 37 GLU cc_start: 0.8089 (mp0) cc_final: 0.7757 (mp0) REVERT: E 76 LYS cc_start: 0.5072 (OUTLIER) cc_final: 0.4689 (pttp) REVERT: E 77 LYS cc_start: 0.7184 (mptt) cc_final: 0.6534 (tppt) REVERT: E 84 THR cc_start: 0.8019 (m) cc_final: 0.7770 (p) REVERT: F 154 GLU cc_start: 0.8231 (tp30) cc_final: 0.7581 (tp30) REVERT: F 155 ASP cc_start: 0.8310 (t0) cc_final: 0.8062 (m-30) REVERT: F 175 ASP cc_start: 0.7690 (m-30) cc_final: 0.7480 (m-30) REVERT: G 80 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7523 (ptt-90) REVERT: H 37 GLU cc_start: 0.7331 (mp0) cc_final: 0.7127 (mp0) REVERT: H 55 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.3219 (mm-30) REVERT: I 76 LYS cc_start: 0.8683 (tttt) cc_final: 0.8344 (mtpt) REVERT: I 188 ASP cc_start: 0.8528 (m-30) cc_final: 0.8223 (m-30) REVERT: J 187 GLU cc_start: 0.7425 (tt0) cc_final: 0.6945 (tp30) REVERT: K 32 LYS cc_start: 0.7374 (mmtm) cc_final: 0.6732 (mmtm) REVERT: K 48 ASP cc_start: 0.8346 (p0) cc_final: 0.8035 (p0) REVERT: K 131 LEU cc_start: 0.8217 (mp) cc_final: 0.7990 (mt) REVERT: K 155 ASP cc_start: 0.8546 (t0) cc_final: 0.8284 (m-30) REVERT: K 158 SER cc_start: 0.9194 (m) cc_final: 0.8880 (t) REVERT: K 174 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6137 (mm) REVERT: K 176 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.4304 (t80) REVERT: L 163 GLU cc_start: 0.5793 (mm-30) cc_final: 0.5134 (mm-30) REVERT: L 246 SER cc_start: 0.8757 (p) cc_final: 0.8387 (p) outliers start: 75 outliers final: 36 residues processed: 410 average time/residue: 0.8076 time to fit residues: 500.1083 Evaluate side-chains 339 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 293 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 176 TYR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 153 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 20.0000 chunk 229 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 324 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 ASN F 177 GLN J 228 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.148810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.111316 restraints weight = 821554.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.113171 restraints weight = 541364.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.111931 restraints weight = 475717.123| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26004 Z= 0.212 Angle : 0.526 4.706 35520 Z= 0.286 Chirality : 0.045 0.313 4080 Planarity : 0.004 0.055 4656 Dihedral : 5.869 43.322 3621 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.01 % Allowed : 15.15 % Favored : 82.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3360 helix: -1.68 (0.33), residues: 216 sheet: -1.15 (0.15), residues: 995 loop : -1.03 (0.12), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 189 HIS 0.003 0.001 HIS E 38 PHE 0.014 0.001 PHE C 257 TYR 0.015 0.001 TYR A 106 ARG 0.005 0.000 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 363 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 2.844 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: A 8 VAL cc_start: 0.8877 (t) cc_final: 0.8392 (m) REVERT: A 32 LYS cc_start: 0.8350 (mttt) cc_final: 0.7365 (mmtm) REVERT: A 49 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7895 (mt) REVERT: A 155 ASP cc_start: 0.7794 (t0) cc_final: 0.7310 (m-30) REVERT: A 259 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8226 (pt) REVERT: B 86 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6786 (mm-30) REVERT: B 199 TYR cc_start: 0.7398 (m-80) cc_final: 0.7178 (m-80) REVERT: D 80 ARG cc_start: 0.7161 (ttp80) cc_final: 0.5398 (ptt-90) REVERT: E 37 GLU cc_start: 0.7932 (mp0) cc_final: 0.7674 (mp0) REVERT: E 76 LYS cc_start: 0.4915 (OUTLIER) cc_final: 0.4635 (pttp) REVERT: E 77 LYS cc_start: 0.7136 (mptt) cc_final: 0.6475 (tppt) REVERT: F 155 ASP cc_start: 0.8289 (t0) cc_final: 0.8019 (m-30) REVERT: H 55 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.2065 (mm-30) REVERT: H 153 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8252 (ptt90) REVERT: I 76 LYS cc_start: 0.8647 (tttt) cc_final: 0.8287 (mtpt) REVERT: I 77 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7853 (tppt) REVERT: I 188 ASP cc_start: 0.8446 (m-30) cc_final: 0.8244 (m-30) REVERT: I 228 ASN cc_start: 0.6872 (p0) cc_final: 0.6603 (p0) REVERT: J 4 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7466 (ttpp) REVERT: J 187 GLU cc_start: 0.7528 (tt0) cc_final: 0.7144 (tp30) REVERT: K 155 ASP cc_start: 0.8455 (t0) cc_final: 0.8190 (m-30) REVERT: K 158 SER cc_start: 0.9125 (m) cc_final: 0.8712 (t) REVERT: K 174 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6043 (mm) REVERT: L 163 GLU cc_start: 0.6038 (mm-30) cc_final: 0.5229 (mm-30) REVERT: L 246 SER cc_start: 0.8789 (p) cc_final: 0.8411 (p) outliers start: 53 outliers final: 34 residues processed: 354 average time/residue: 0.8187 time to fit residues: 441.5446 Evaluate side-chains 316 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 153 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 224 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 291 optimal weight: 0.0970 chunk 81 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.146286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.109000 restraints weight = 828775.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.109727 restraints weight = 562973.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.109233 restraints weight = 498282.103| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26004 Z= 0.410 Angle : 0.580 6.559 35520 Z= 0.318 Chirality : 0.048 0.310 4080 Planarity : 0.004 0.054 4656 Dihedral : 5.862 43.062 3621 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.92 % Allowed : 14.81 % Favored : 82.27 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 3360 helix: -1.49 (0.33), residues: 225 sheet: -1.27 (0.15), residues: 989 loop : -1.15 (0.12), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 189 HIS 0.004 0.001 HIS L 145 PHE 0.014 0.002 PHE F 173 TYR 0.018 0.002 TYR A 106 ARG 0.004 0.001 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 288 time to evaluate : 2.854 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 8 VAL cc_start: 0.8709 (t) cc_final: 0.8342 (m) REVERT: A 32 LYS cc_start: 0.8434 (mttt) cc_final: 0.7508 (mmtm) REVERT: A 49 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7913 (mt) REVERT: A 154 GLU cc_start: 0.8058 (tp30) cc_final: 0.7673 (tp30) REVERT: A 155 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: A 259 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8252 (pt) REVERT: B 49 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8208 (tp) REVERT: B 86 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6724 (mm-30) REVERT: C 69 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6838 (pt0) REVERT: E 37 GLU cc_start: 0.8021 (mp0) cc_final: 0.7701 (mp0) REVERT: E 76 LYS cc_start: 0.5003 (OUTLIER) cc_final: 0.4696 (pttp) REVERT: E 77 LYS cc_start: 0.7241 (mptt) cc_final: 0.6634 (tppt) REVERT: F 140 VAL cc_start: 0.8935 (p) cc_final: 0.8616 (m) REVERT: F 155 ASP cc_start: 0.8143 (t0) cc_final: 0.7927 (m-30) REVERT: G 80 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7428 (ptt-90) REVERT: G 187 GLU cc_start: 0.8093 (tt0) cc_final: 0.7861 (tp30) REVERT: H 55 GLU cc_start: 0.5448 (OUTLIER) cc_final: 0.2919 (mm-30) REVERT: H 153 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8235 (ptt90) REVERT: I 31 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8389 (mp) REVERT: I 76 LYS cc_start: 0.8725 (tttt) cc_final: 0.8301 (mtpt) REVERT: I 77 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7935 (tppt) REVERT: I 228 ASN cc_start: 0.6681 (p0) cc_final: 0.6468 (p0) REVERT: J 55 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.4887 (mt-10) REVERT: J 139 ASP cc_start: 0.7839 (p0) cc_final: 0.7373 (p0) REVERT: J 187 GLU cc_start: 0.7622 (tt0) cc_final: 0.7099 (tp30) REVERT: K 155 ASP cc_start: 0.8594 (t0) cc_final: 0.8276 (m-30) REVERT: K 158 SER cc_start: 0.9268 (m) cc_final: 0.8809 (t) REVERT: K 174 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6188 (mm) REVERT: K 176 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.4392 (t80) REVERT: K 183 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: L 85 GLU cc_start: 0.8022 (mp0) cc_final: 0.7804 (mp0) REVERT: L 163 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5429 (mm-30) outliers start: 77 outliers final: 48 residues processed: 346 average time/residue: 0.7736 time to fit residues: 400.6407 Evaluate side-chains 330 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 267 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 176 TYR Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.146111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.108562 restraints weight = 827606.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.109426 restraints weight = 549228.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.108773 restraints weight = 494817.128| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26004 Z= 0.352 Angle : 0.547 5.051 35520 Z= 0.297 Chirality : 0.047 0.312 4080 Planarity : 0.004 0.058 4656 Dihedral : 5.676 41.274 3621 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.03 % Allowed : 15.61 % Favored : 81.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 3360 helix: -1.36 (0.35), residues: 220 sheet: -1.30 (0.15), residues: 991 loop : -1.20 (0.12), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 189 HIS 0.004 0.001 HIS E 38 PHE 0.013 0.002 PHE G 144 TYR 0.016 0.002 TYR L 182 ARG 0.004 0.001 ARG K 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 368 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 288 time to evaluate : 2.918 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: A 8 VAL cc_start: 0.8619 (t) cc_final: 0.8327 (m) REVERT: A 32 LYS cc_start: 0.8444 (mttt) cc_final: 0.7407 (mmtm) REVERT: A 49 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 154 GLU cc_start: 0.8091 (tp30) cc_final: 0.7715 (tp30) REVERT: A 155 ASP cc_start: 0.7982 (t0) cc_final: 0.7566 (m-30) REVERT: A 259 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8243 (pt) REVERT: B 49 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8235 (tp) REVERT: B 86 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6752 (mm-30) REVERT: B 111 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: C 69 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6298 (mm-30) REVERT: E 37 GLU cc_start: 0.7817 (mp0) cc_final: 0.7526 (mp0) REVERT: E 76 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.4614 (pttp) REVERT: E 77 LYS cc_start: 0.7270 (mptt) cc_final: 0.6614 (tppt) REVERT: G 80 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7508 (ptt-90) REVERT: H 55 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.3009 (mm-30) REVERT: I 76 LYS cc_start: 0.8647 (tttt) cc_final: 0.8211 (mtpt) REVERT: I 77 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8092 (tppt) REVERT: I 129 ARG cc_start: 0.8626 (ptm160) cc_final: 0.8223 (ptp90) REVERT: I 228 ASN cc_start: 0.6825 (p0) cc_final: 0.6520 (p0) REVERT: J 4 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7427 (ttpp) REVERT: J 55 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.4860 (mt-10) REVERT: J 81 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7103 (mp0) REVERT: K 155 ASP cc_start: 0.8518 (t0) cc_final: 0.8256 (m-30) REVERT: K 158 SER cc_start: 0.9295 (m) cc_final: 0.8778 (t) REVERT: K 174 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6227 (mm) REVERT: K 176 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.4338 (t80) REVERT: K 183 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6780 (pt0) REVERT: L 85 GLU cc_start: 0.8056 (mp0) cc_final: 0.7815 (mp0) REVERT: L 163 GLU cc_start: 0.6025 (mm-30) cc_final: 0.5493 (mm-30) outliers start: 80 outliers final: 51 residues processed: 349 average time/residue: 0.7499 time to fit residues: 397.2225 Evaluate side-chains 325 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 176 TYR Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 181 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 ASN F 177 GLN I 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.147457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.109932 restraints weight = 819271.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.111066 restraints weight = 542491.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.110590 restraints weight = 482533.784| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26004 Z= 0.235 Angle : 0.499 4.562 35520 Z= 0.270 Chirality : 0.045 0.312 4080 Planarity : 0.004 0.055 4656 Dihedral : 5.349 39.910 3621 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.50 % Allowed : 16.17 % Favored : 81.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3360 helix: -1.13 (0.36), residues: 214 sheet: -1.18 (0.15), residues: 1003 loop : -1.10 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 189 HIS 0.003 0.001 HIS E 38 PHE 0.012 0.001 PHE G 144 TYR 0.015 0.001 TYR L 182 ARG 0.003 0.000 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 2.886 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: A 32 LYS cc_start: 0.8219 (mttt) cc_final: 0.7285 (mmtm) REVERT: A 49 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7794 (mt) REVERT: A 154 GLU cc_start: 0.8148 (tp30) cc_final: 0.7704 (tp30) REVERT: A 155 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: A 259 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8281 (pt) REVERT: B 49 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8136 (tp) REVERT: B 86 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: B 111 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: C 69 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6449 (mm-30) REVERT: C 182 TYR cc_start: 0.9119 (p90) cc_final: 0.8914 (p90) REVERT: C 267 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8146 (mp) REVERT: E 37 GLU cc_start: 0.7908 (mp0) cc_final: 0.7701 (mp0) REVERT: E 77 LYS cc_start: 0.7213 (mptt) cc_final: 0.6645 (ttpp) REVERT: G 80 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7520 (ptt-90) REVERT: H 55 GLU cc_start: 0.5604 (OUTLIER) cc_final: 0.3028 (mm-30) REVERT: I 77 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8215 (tppt) REVERT: I 129 ARG cc_start: 0.8642 (ptm160) cc_final: 0.8249 (ptp90) REVERT: I 228 ASN cc_start: 0.6957 (p0) cc_final: 0.6672 (p0) REVERT: J 4 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7474 (ttpp) REVERT: J 81 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7070 (mp0) REVERT: J 139 ASP cc_start: 0.7086 (p0) cc_final: 0.6506 (p0) REVERT: K 155 ASP cc_start: 0.8475 (t0) cc_final: 0.8217 (m-30) REVERT: K 158 SER cc_start: 0.9275 (m) cc_final: 0.8744 (t) REVERT: K 174 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6128 (mm) REVERT: K 176 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.4485 (t80) REVERT: L 85 GLU cc_start: 0.8127 (mp0) cc_final: 0.7861 (mp0) REVERT: L 163 GLU cc_start: 0.6195 (mm-30) cc_final: 0.5479 (mm-30) outliers start: 66 outliers final: 43 residues processed: 327 average time/residue: 0.8296 time to fit residues: 406.9856 Evaluate side-chains 326 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 271 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 176 TYR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.145893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.108455 restraints weight = 823944.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.109367 restraints weight = 559094.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.108656 restraints weight = 499409.880| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.6905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26004 Z= 0.342 Angle : 0.533 4.783 35520 Z= 0.289 Chirality : 0.046 0.309 4080 Planarity : 0.004 0.056 4656 Dihedral : 5.460 40.691 3621 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.88 % Allowed : 16.40 % Favored : 80.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3360 helix: -1.03 (0.36), residues: 214 sheet: -1.24 (0.15), residues: 1004 loop : -1.14 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 42 HIS 0.003 0.001 HIS B 145 PHE 0.012 0.002 PHE F 190 TYR 0.017 0.001 TYR L 182 ARG 0.003 0.001 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 353 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 277 time to evaluate : 2.879 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: A 49 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7889 (mt) REVERT: A 71 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6238 (ppt170) REVERT: A 154 GLU cc_start: 0.8243 (tp30) cc_final: 0.7773 (tp30) REVERT: A 155 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: A 259 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8263 (pt) REVERT: B 49 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8230 (tp) REVERT: B 86 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: B 111 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: C 69 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6199 (mm-30) REVERT: E 37 GLU cc_start: 0.7938 (mp0) cc_final: 0.7642 (mp0) REVERT: E 77 LYS cc_start: 0.7575 (mptt) cc_final: 0.6866 (ttpp) REVERT: G 80 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7534 (ptt-90) REVERT: H 55 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.4353 (mt-10) REVERT: I 69 GLU cc_start: 0.7636 (tt0) cc_final: 0.7388 (mt-10) REVERT: I 77 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8237 (tppt) REVERT: I 228 ASN cc_start: 0.6750 (p0) cc_final: 0.6545 (p0) REVERT: J 4 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7474 (ttpp) REVERT: J 55 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.4712 (mt-10) REVERT: J 81 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7184 (mp0) REVERT: K 155 ASP cc_start: 0.8513 (t0) cc_final: 0.8258 (m-30) REVERT: K 158 SER cc_start: 0.9301 (m) cc_final: 0.8807 (t) REVERT: K 174 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6103 (mm) REVERT: K 176 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.4417 (t80) REVERT: K 183 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6743 (pt0) REVERT: L 85 GLU cc_start: 0.8075 (mp0) cc_final: 0.7656 (mp0) REVERT: L 163 GLU cc_start: 0.6140 (mm-30) cc_final: 0.5468 (mm-30) outliers start: 76 outliers final: 55 residues processed: 337 average time/residue: 0.7786 time to fit residues: 397.0377 Evaluate side-chains 337 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 268 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 176 TYR Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 301 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 chunk 92 optimal weight: 0.0170 chunk 272 optimal weight: 0.0970 chunk 285 optimal weight: 0.9990 chunk 300 optimal weight: 20.0000 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.148842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.112239 restraints weight = 816378.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.112856 restraints weight = 550635.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.112536 restraints weight = 491335.890| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26004 Z= 0.138 Angle : 0.469 4.582 35520 Z= 0.252 Chirality : 0.045 0.313 4080 Planarity : 0.003 0.053 4656 Dihedral : 5.061 38.979 3621 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.78 % Allowed : 17.46 % Favored : 80.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3360 helix: -0.95 (0.37), residues: 214 sheet: -0.98 (0.15), residues: 1007 loop : -0.99 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 189 HIS 0.002 0.000 HIS B 52 PHE 0.011 0.001 PHE C 257 TYR 0.013 0.001 TYR L 182 ARG 0.004 0.000 ARG H 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 330 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 2.932 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: A 45 THR cc_start: 0.8147 (t) cc_final: 0.7821 (t) REVERT: A 48 ASP cc_start: 0.7390 (p0) cc_final: 0.7061 (p0) REVERT: A 49 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7770 (mt) REVERT: A 71 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6296 (ppt170) REVERT: A 154 GLU cc_start: 0.8121 (tp30) cc_final: 0.7643 (tp30) REVERT: A 155 ASP cc_start: 0.7668 (t0) cc_final: 0.7283 (m-30) REVERT: B 86 GLU cc_start: 0.7045 (pp20) cc_final: 0.6699 (mm-30) REVERT: C 225 TYR cc_start: 0.7996 (p90) cc_final: 0.7695 (p90) REVERT: E 4 LYS cc_start: 0.7632 (mtmt) cc_final: 0.7273 (mtmm) REVERT: E 37 GLU cc_start: 0.7813 (mp0) cc_final: 0.7574 (mp0) REVERT: E 77 LYS cc_start: 0.7380 (mptt) cc_final: 0.6836 (ttpp) REVERT: E 154 GLU cc_start: 0.8416 (tp30) cc_final: 0.7728 (tp30) REVERT: H 55 GLU cc_start: 0.5478 (OUTLIER) cc_final: 0.3072 (mm-30) REVERT: H 138 ASN cc_start: 0.7869 (m-40) cc_final: 0.7641 (m-40) REVERT: H 154 GLU cc_start: 0.7906 (tp30) cc_final: 0.7705 (tp30) REVERT: I 69 GLU cc_start: 0.7612 (tt0) cc_final: 0.7369 (mt-10) REVERT: I 77 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8190 (tppt) REVERT: J 55 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.4581 (mt-10) REVERT: J 81 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7140 (mp0) REVERT: J 138 ASN cc_start: 0.7159 (p0) cc_final: 0.6743 (p0) REVERT: J 139 ASP cc_start: 0.6904 (p0) cc_final: 0.5869 (p0) REVERT: K 155 ASP cc_start: 0.8493 (t0) cc_final: 0.8254 (m-30) REVERT: K 158 SER cc_start: 0.9240 (m) cc_final: 0.8688 (t) REVERT: K 174 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6065 (mm) REVERT: K 176 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.4414 (t80) REVERT: K 183 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: L 85 GLU cc_start: 0.8166 (mp0) cc_final: 0.7829 (mp0) REVERT: L 163 GLU cc_start: 0.5841 (mm-30) cc_final: 0.5285 (mm-30) outliers start: 47 outliers final: 35 residues processed: 322 average time/residue: 0.8336 time to fit residues: 407.3355 Evaluate side-chains 315 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 176 TYR Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 1.9990 chunk 319 optimal weight: 0.4980 chunk 194 optimal weight: 4.9990 chunk 151 optimal weight: 0.2980 chunk 221 optimal weight: 20.0000 chunk 334 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.146469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.109275 restraints weight = 816407.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.110255 restraints weight = 546867.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.109388 restraints weight = 496595.960| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26004 Z= 0.307 Angle : 0.514 4.661 35520 Z= 0.278 Chirality : 0.046 0.311 4080 Planarity : 0.004 0.055 4656 Dihedral : 5.228 40.426 3621 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.89 % Allowed : 17.54 % Favored : 80.57 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3360 helix: -0.94 (0.36), residues: 214 sheet: -1.10 (0.15), residues: 1007 loop : -1.07 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 189 HIS 0.003 0.001 HIS L 145 PHE 0.012 0.001 PHE J 144 TYR 0.016 0.001 TYR L 182 ARG 0.003 0.000 ARG G 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Evaluate side-chains 329 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 2.847 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 45 THR cc_start: 0.8124 (t) cc_final: 0.7774 (t) REVERT: A 49 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7920 (mt) REVERT: A 71 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6275 (ppt170) REVERT: A 154 GLU cc_start: 0.8134 (tp30) cc_final: 0.7610 (tp30) REVERT: A 155 ASP cc_start: 0.7991 (t0) cc_final: 0.7542 (m-30) REVERT: B 86 GLU cc_start: 0.7142 (pp20) cc_final: 0.6690 (mm-30) REVERT: B 111 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: D 80 ARG cc_start: 0.7409 (ttp80) cc_final: 0.5465 (ptt-90) REVERT: E 4 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7516 (mtmm) REVERT: E 37 GLU cc_start: 0.7906 (mp0) cc_final: 0.7646 (mp0) REVERT: E 77 LYS cc_start: 0.7271 (mptt) cc_final: 0.6581 (ttpp) REVERT: H 55 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.2719 (mm-30) REVERT: I 69 GLU cc_start: 0.7666 (tt0) cc_final: 0.7426 (mt-10) REVERT: I 77 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8133 (tppt) REVERT: J 55 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.4402 (mt-10) REVERT: J 81 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7228 (mp0) REVERT: J 138 ASN cc_start: 0.7312 (p0) cc_final: 0.6889 (p0) REVERT: J 139 ASP cc_start: 0.7009 (p0) cc_final: 0.6076 (p0) REVERT: K 155 ASP cc_start: 0.8440 (t0) cc_final: 0.8201 (m-30) REVERT: K 158 SER cc_start: 0.9294 (m) cc_final: 0.8750 (t) REVERT: K 174 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6180 (mm) REVERT: K 176 TYR cc_start: 0.6183 (OUTLIER) cc_final: 0.4468 (t80) REVERT: K 183 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6673 (pt0) REVERT: L 85 GLU cc_start: 0.8051 (mp0) cc_final: 0.7645 (mp0) REVERT: L 163 GLU cc_start: 0.5866 (mm-30) cc_final: 0.5236 (mm-30) outliers start: 50 outliers final: 38 residues processed: 323 average time/residue: 0.8173 time to fit residues: 396.5659 Evaluate side-chains 314 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 LEU Chi-restraints excluded: chain K residue 176 TYR Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 274 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.148448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.111906 restraints weight = 818926.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.112537 restraints weight = 564077.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.112156 restraints weight = 505566.958| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26004 Z= 0.202 Angle : 0.477 4.477 35520 Z= 0.256 Chirality : 0.045 0.313 4080 Planarity : 0.003 0.054 4656 Dihedral : 5.028 39.760 3621 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.63 % Allowed : 17.92 % Favored : 80.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3360 helix: -0.95 (0.36), residues: 214 sheet: -1.01 (0.15), residues: 1008 loop : -1.03 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 189 HIS 0.003 0.001 HIS E 38 PHE 0.010 0.001 PHE C 257 TYR 0.015 0.001 TYR L 182 ARG 0.003 0.000 ARG H 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10856.97 seconds wall clock time: 187 minutes 2.35 seconds (11222.35 seconds total)