Starting phenix.real_space_refine on Sat Sep 12 07:35:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3j8i_6179/09_2026/3j8i_6179.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j8i_6179/09_2026/3j8i_6179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2026/3j8i_6179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2026/3j8i_6179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2026/3j8i_6179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2026/3j8i_6179.map" restraint_files = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2026/3j8i_6179.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2026/3j8i_6179.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.009 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9320 2.51 5 N 2490 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14800 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "F" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "H" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.34, per 1000 atoms: 0.23 Number of scatterers: 14800 At special positions: 0 Unit cell: (110.25, 86.1, 194.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2870 8.00 N 2490 7.00 C 9320 6.00 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: 1.16 Conformation dependent library (CDL) restraints added in 661.4 milliseconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 15 sheets defined 40.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 82 through 91 removed outlier: 3.859A pdb=" N TRP D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.049A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 4.118A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 210 Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.595A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.979A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.724A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.790A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.522A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 360 through 365 Processing helix chain 'D' and resid 366 through 372 removed outlier: 4.074A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.867A pdb=" N TRP E 86 " --> pdb=" O MET E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 127 removed outlier: 4.047A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 removed outlier: 4.065A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 210 Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.605A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 263 removed outlier: 3.967A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Proline residue: E 258 - end of helix removed outlier: 4.633A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.811A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.537A pdb=" N THR E 318 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 360 through 365 Processing helix chain 'E' and resid 366 through 372 removed outlier: 4.078A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 82 through 91 removed outlier: 3.889A pdb=" N TRP F 86 " --> pdb=" O MET F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.073A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 removed outlier: 4.079A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 210 Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'F' and resid 223 through 233 removed outlier: 3.601A pdb=" N ALA F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.949A pdb=" N ARG F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.725A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 284 removed outlier: 3.851A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 282 " --> pdb=" O THR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 296 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.609A pdb=" N THR F 318 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 360 through 365 Processing helix chain 'F' and resid 366 through 372 removed outlier: 4.068A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.859A pdb=" N TRP G 86 " --> pdb=" O MET G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.059A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 144 removed outlier: 4.050A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 4.289A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 202 through 210 Processing helix chain 'G' and resid 211 through 216 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.619A pdb=" N ALA G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.972A pdb=" N ARG G 256 " --> pdb=" O ASN G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 removed outlier: 3.709A pdb=" N PHE G 262 " --> pdb=" O PRO G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 284 removed outlier: 3.767A pdb=" N TYR G 279 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 296 Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.570A pdb=" N THR G 318 " --> pdb=" O GLN G 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 320 " --> pdb=" O GLU G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 352 through 356 removed outlier: 3.647A pdb=" N MET G 355 " --> pdb=" O PHE G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 365 Processing helix chain 'G' and resid 366 through 372 removed outlier: 4.086A pdb=" N VAL G 370 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.868A pdb=" N TRP H 86 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 127 removed outlier: 4.059A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 removed outlier: 4.079A pdb=" N SER H 141 " --> pdb=" O GLN H 137 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 202 through 210 Processing helix chain 'H' and resid 211 through 216 Processing helix chain 'H' and resid 223 through 233 removed outlier: 3.605A pdb=" N ALA H 228 " --> pdb=" O GLU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 263 removed outlier: 3.997A pdb=" N ARG H 256 " --> pdb=" O ASN H 252 " (cutoff:3.500A) Proline residue: H 258 - end of helix removed outlier: 4.594A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 284 removed outlier: 3.871A pdb=" N TYR H 279 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.560A pdb=" N THR H 318 " --> pdb=" O GLN H 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 Processing helix chain 'H' and resid 360 through 365 Processing helix chain 'H' and resid 366 through 372 removed outlier: 4.036A pdb=" N VAL H 370 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS H 371 " --> pdb=" O PRO H 367 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.572A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=C, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.631A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.596A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=F, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.629A pdb=" N VAL E 163 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.614A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=I, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.608A pdb=" N VAL F 163 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 152 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.589A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=L, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.649A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL G 152 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.609A pdb=" N THR H 106 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=O, first strand: chain 'H' and resid 169 through 170 removed outlier: 3.643A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4526 1.34 - 1.48: 4024 1.48 - 1.63: 6385 1.63 - 1.77: 21 1.77 - 1.91: 164 Bond restraints: 15120 Sorted by residual: bond pdb=" C LEU D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.331 1.383 -0.052 7.90e-03 1.60e+04 4.29e+01 bond pdb=" C LEU H 171 " pdb=" N PRO H 172 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.05e+01 bond pdb=" C LEU F 171 " pdb=" N PRO F 172 " ideal model delta sigma weight residual 1.331 1.379 -0.047 7.90e-03 1.60e+04 3.55e+01 bond pdb=" CA ILE E 250 " pdb=" C ILE E 250 " ideal model delta sigma weight residual 1.526 1.474 0.052 9.00e-03 1.23e+04 3.32e+01 bond pdb=" C LEU E 171 " pdb=" N PRO E 172 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.24e+01 ... (remaining 15115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18152 2.36 - 4.72: 1921 4.72 - 7.08: 359 7.08 - 9.44: 54 9.44 - 11.80: 29 Bond angle restraints: 20515 Sorted by residual: angle pdb=" C VAL F 129 " pdb=" N PRO F 130 " pdb=" CA PRO F 130 " ideal model delta sigma weight residual 119.19 126.79 -7.60 1.06e+00 8.90e-01 5.13e+01 angle pdb=" C ALA D 108 " pdb=" N PRO D 109 " pdb=" CA PRO D 109 " ideal model delta sigma weight residual 119.78 127.02 -7.24 1.03e+00 9.43e-01 4.94e+01 angle pdb=" N ALA G 138 " pdb=" CA ALA G 138 " pdb=" C ALA G 138 " ideal model delta sigma weight residual 111.28 118.53 -7.25 1.09e+00 8.42e-01 4.42e+01 angle pdb=" C ALA G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta sigma weight residual 119.78 126.55 -6.77 1.03e+00 9.43e-01 4.32e+01 angle pdb=" N ALA D 138 " pdb=" CA ALA D 138 " pdb=" C ALA D 138 " ideal model delta sigma weight residual 111.36 118.09 -6.73 1.09e+00 8.42e-01 3.81e+01 ... (remaining 20510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8650 35.49 - 70.97: 411 70.97 - 106.46: 34 106.46 - 141.94: 5 141.94 - 177.43: 5 Dihedral angle restraints: 9105 sinusoidal: 3685 harmonic: 5420 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.33 -177.32 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 9102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1407 0.093 - 0.185: 657 0.185 - 0.278: 181 0.278 - 0.370: 24 0.370 - 0.463: 6 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO E 243 " pdb=" N PRO E 243 " pdb=" C PRO E 243 " pdb=" CB PRO E 243 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA PRO F 243 " pdb=" N PRO F 243 " pdb=" C PRO F 243 " pdb=" CB PRO F 243 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CA PRO H 243 " pdb=" N PRO H 243 " pdb=" C PRO H 243 " pdb=" CB PRO H 243 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 2272 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 166 " -0.071 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR D 166 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 166 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 166 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR D 166 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 166 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D 166 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 166 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 166 " 0.061 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR E 166 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR E 166 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 166 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR E 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 166 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 166 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 166 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 166 " -0.060 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR H 166 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR H 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 166 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR H 166 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 166 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR H 166 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR H 166 " -0.027 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 784 2.68 - 3.24: 16908 3.24 - 3.79: 24664 3.79 - 4.35: 32343 4.35 - 4.90: 50125 Nonbonded interactions: 124824 Sorted by model distance: nonbonded pdb=" O SER F 350 " pdb=" N PHE F 352 " model vdw 2.125 3.120 nonbonded pdb=" O TYR H 362 " pdb=" O ALA H 365 " model vdw 2.131 3.040 nonbonded pdb=" O TYR F 362 " pdb=" O ALA F 365 " model vdw 2.140 3.040 nonbonded pdb=" O TYR G 362 " pdb=" O ALA G 365 " model vdw 2.154 3.040 nonbonded pdb=" O SER D 350 " pdb=" N PHE D 352 " model vdw 2.160 3.120 ... (remaining 124819 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: 0.05 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.018 0.120 15120 Z= 0.963 Angle : 1.668 11.796 20515 Z= 1.105 Chirality : 0.109 0.463 2275 Planarity : 0.007 0.098 2630 Dihedral : 19.470 177.430 5635 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 76.17 Ramachandran Plot: Outliers : 6.06 % Allowed : 6.43 % Favored : 87.51 % Rotamer: Outliers : 14.53 % Allowed : 14.65 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.17), residues: 1865 helix: -0.26 (0.22), residues: 500 sheet: 0.08 (0.37), residues: 205 loop : -1.71 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG E 290 TYR 0.071 0.009 TYR D 166 PHE 0.030 0.005 PHE G 375 TRP 0.041 0.009 TRP G 356 HIS 0.004 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01773 / 0.96 (15120) covalent geometry : angle 1.66809 / 1.10 (20515) hydrogen bonds : bond 0.29858 / 20.64 ( 419) hydrogen bonds : angle 10.71833 / 7.58 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 60 time to evaluate : 0.109 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: D 76 ILE cc_start: 0.8806 (mt) cc_final: 0.8105 (mt) REVERT: D 82 MET cc_start: 0.8828 (ttt) cc_final: 0.8509 (ttm) REVERT: D 116 ARG cc_start: 0.6769 (mtp180) cc_final: 0.6181 (mtp-110) REVERT: D 147 ARG cc_start: 0.7676 (mpp-170) cc_final: 0.7265 (mpp-170) REVERT: D 371 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7148 (t-90) REVERT: D 373 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6278 (tmmt) outliers start: 46 outliers final: 19 residues processed: 96 average time/residue: 0.0654 time to fit residues: 7.5508 Evaluate side-chains 60 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.0060 chunk 149 optimal weight: 8.9990 overall best weight: 2.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 GLN D 87 HIS ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 296 ASN D 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062376 restraints weight = 15136.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063788 restraints weight = 9136.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064920 restraints weight = 6160.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.065611 restraints weight = 4440.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066157 restraints weight = 3438.053| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15120 Z= 0.175 Angle : 0.943 9.479 20515 Z= 0.470 Chirality : 0.049 0.194 2275 Planarity : 0.006 0.040 2630 Dihedral : 8.561 115.365 2095 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 1.88 % Allowed : 10.72 % Favored : 87.40 % Rotamer: Outliers : 0.31 % Allowed : 7.86 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1865 helix: 0.06 (0.20), residues: 645 sheet: 0.10 (0.38), residues: 220 loop : -2.19 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 254 TYR 0.026 0.002 TYR G 169 PHE 0.011 0.002 PHE D 262 TRP 0.013 0.002 TRP F 79 HIS 0.009 0.002 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (15120) covalent geometry : angle 0.94252 / 0.47 (20515) hydrogen bonds : bond 0.05566 / 3.78 ( 419) hydrogen bonds : angle 6.22046 / 4.42 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 66 THR cc_start: 0.7601 (m) cc_final: 0.7291 (t) REVERT: F 67 LEU cc_start: 0.9020 (mp) cc_final: 0.8565 (mp) REVERT: F 116 ARG cc_start: 0.6860 (mtp180) cc_final: 0.6566 (mtp-110) REVERT: F 134 VAL cc_start: 0.8600 (t) cc_final: 0.7935 (t) REVERT: F 147 ARG cc_start: 0.7363 (mpp-170) cc_final: 0.6753 (mpp-170) REVERT: F 184 ASP cc_start: 0.8378 (p0) cc_final: 0.7855 (t70) REVERT: F 211 ASP cc_start: 0.7896 (p0) cc_final: 0.6141 (t0) REVERT: F 223 PHE cc_start: 0.7799 (t80) cc_final: 0.7582 (t80) REVERT: F 227 MET cc_start: 0.7920 (ttm) cc_final: 0.7694 (ttm) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.0607 time to fit residues: 5.2152 Evaluate side-chains 50 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 149 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 59 GLN F 87 HIS ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 162 ASN F 314 GLN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.062727 restraints weight = 16045.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063917 restraints weight = 10076.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.064800 restraints weight = 6891.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065302 restraints weight = 5052.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065775 restraints weight = 4016.902| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15120 Z= 0.163 Angle : 0.835 7.991 20515 Z= 0.418 Chirality : 0.046 0.162 2275 Planarity : 0.005 0.046 2630 Dihedral : 7.618 94.931 2095 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.72 % Favored : 87.94 % Rotamer: Outliers : 0.31 % Allowed : 7.23 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.18), residues: 1865 helix: -0.36 (0.19), residues: 680 sheet: -0.05 (0.37), residues: 230 loop : -2.02 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 254 TYR 0.010 0.001 TYR D 294 PHE 0.021 0.002 PHE G 200 TRP 0.015 0.002 TRP E 79 HIS 0.004 0.001 HIS G 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (15120) covalent geometry : angle 0.83493 / 0.42 (20515) hydrogen bonds : bond 0.04654 / 3.16 ( 419) hydrogen bonds : angle 6.05911 / 4.30 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 66 THR cc_start: 0.7723 (m) cc_final: 0.7476 (t) REVERT: F 67 LEU cc_start: 0.8987 (mp) cc_final: 0.8459 (mp) REVERT: F 72 GLU cc_start: 0.8316 (tp30) cc_final: 0.8018 (mt-10) REVERT: F 184 ASP cc_start: 0.8293 (p0) cc_final: 0.7786 (t0) REVERT: F 211 ASP cc_start: 0.7874 (p0) cc_final: 0.6891 (t0) REVERT: F 269 MET cc_start: 0.7281 (mpp) cc_final: 0.6819 (mmp) REVERT: F 296 ASN cc_start: 0.7810 (m-40) cc_final: 0.7306 (m-40) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0694 time to fit residues: 5.0329 Evaluate side-chains 45 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 176 optimal weight: 10.0000 chunk 51 optimal weight: 0.2980 chunk 110 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 181 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 126 optimal weight: 30.0000 chunk 153 optimal weight: 30.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.068433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.062766 restraints weight = 16212.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.063975 restraints weight = 10064.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064831 restraints weight = 6766.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065446 restraints weight = 4897.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065764 restraints weight = 3752.716| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15120 Z= 0.161 Angle : 0.825 9.978 20515 Z= 0.414 Chirality : 0.045 0.158 2275 Planarity : 0.006 0.055 2630 Dihedral : 6.912 67.223 2095 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.46 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.18), residues: 1865 helix: -0.31 (0.19), residues: 690 sheet: -0.32 (0.35), residues: 230 loop : -1.95 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 147 TYR 0.008 0.001 TYR F 362 PHE 0.015 0.001 PHE D 262 TRP 0.018 0.002 TRP H 79 HIS 0.003 0.001 HIS G 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (15120) covalent geometry : angle 0.82490 / 0.41 (20515) hydrogen bonds : bond 0.04215 / 2.84 ( 419) hydrogen bonds : angle 5.75993 / 4.09 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 9 VAL cc_start: 0.7759 (t) cc_final: 0.7003 (t) REVERT: F 25 ASP cc_start: 0.7814 (m-30) cc_final: 0.7479 (p0) REVERT: F 67 LEU cc_start: 0.8870 (mp) cc_final: 0.8561 (mp) REVERT: F 104 LEU cc_start: 0.8380 (tp) cc_final: 0.8070 (pp) REVERT: F 105 LEU cc_start: 0.6834 (mp) cc_final: 0.6533 (tp) REVERT: F 211 ASP cc_start: 0.7898 (p0) cc_final: 0.6924 (t0) REVERT: F 217 CYS cc_start: 0.6215 (p) cc_final: 0.5637 (p) REVERT: F 269 MET cc_start: 0.7932 (mpp) cc_final: 0.7656 (mmm) REVERT: F 299 MET cc_start: 0.8169 (ptm) cc_final: 0.7901 (ptm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0489 time to fit residues: 3.4720 Evaluate side-chains 44 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 160 optimal weight: 0.0570 chunk 29 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 163 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 overall best weight: 3.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN F 173 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062647 restraints weight = 14554.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063979 restraints weight = 8896.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064962 restraints weight = 5929.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065636 restraints weight = 4185.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066082 restraints weight = 3121.319| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15120 Z= 0.145 Angle : 0.795 7.557 20515 Z= 0.400 Chirality : 0.045 0.154 2275 Planarity : 0.005 0.046 2630 Dihedral : 6.379 49.516 2095 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 1.34 % Allowed : 11.80 % Favored : 86.86 % Rotamer: Outliers : 0.31 % Allowed : 3.46 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 1865 helix: -0.13 (0.20), residues: 655 sheet: -0.45 (0.35), residues: 245 loop : -1.92 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 256 TYR 0.012 0.001 TYR F 166 PHE 0.012 0.002 PHE E 200 TRP 0.019 0.002 TRP H 79 HIS 0.004 0.001 HIS F 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (15120) covalent geometry : angle 0.79469 / 0.40 (20515) hydrogen bonds : bond 0.03797 / 2.55 ( 419) hydrogen bonds : angle 6.04666 / 4.34 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6717 (mmp) cc_final: 0.4245 (mtm) REVERT: F 67 LEU cc_start: 0.8913 (mp) cc_final: 0.8559 (mp) REVERT: F 184 ASP cc_start: 0.8122 (p0) cc_final: 0.7457 (t70) REVERT: F 211 ASP cc_start: 0.7923 (p0) cc_final: 0.6867 (t0) REVERT: F 227 MET cc_start: 0.7824 (ttm) cc_final: 0.7572 (ttm) REVERT: F 257 CYS cc_start: 0.8816 (p) cc_final: 0.8509 (m) REVERT: F 269 MET cc_start: 0.7759 (mpp) cc_final: 0.7273 (mmp) REVERT: F 299 MET cc_start: 0.8104 (ptm) cc_final: 0.7080 (ptp) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0548 time to fit residues: 3.9556 Evaluate side-chains 42 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 150 optimal weight: 0.0000 chunk 180 optimal weight: 20.0000 chunk 99 optimal weight: 0.0020 chunk 168 optimal weight: 20.0000 chunk 1 optimal weight: 40.0000 chunk 125 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 overall best weight: 2.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.062974 restraints weight = 15140.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.064280 restraints weight = 9354.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065296 restraints weight = 6337.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065956 restraints weight = 4552.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066420 restraints weight = 3447.882| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15120 Z= 0.135 Angle : 0.811 11.078 20515 Z= 0.404 Chirality : 0.044 0.164 2275 Planarity : 0.005 0.046 2630 Dihedral : 5.985 40.028 2095 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.46 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 1865 helix: 0.09 (0.20), residues: 625 sheet: -0.37 (0.35), residues: 250 loop : -1.81 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 147 TYR 0.012 0.001 TYR E 166 PHE 0.012 0.001 PHE E 200 TRP 0.022 0.002 TRP H 79 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15120) covalent geometry : angle 0.81082 / 0.40 (20515) hydrogen bonds : bond 0.03850 / 2.55 ( 419) hydrogen bonds : angle 5.88000 / 4.20 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.8885 (mp) cc_final: 0.8579 (mp) REVERT: F 104 LEU cc_start: 0.8558 (tp) cc_final: 0.8337 (tp) REVERT: F 111 ASN cc_start: 0.5399 (t0) cc_final: 0.5114 (t0) REVERT: F 184 ASP cc_start: 0.8066 (p0) cc_final: 0.7418 (t70) REVERT: F 196 ARG cc_start: 0.8288 (mmt180) cc_final: 0.7740 (mmt90) REVERT: F 211 ASP cc_start: 0.7781 (p0) cc_final: 0.6948 (t0) REVERT: F 257 CYS cc_start: 0.8701 (p) cc_final: 0.8484 (m) REVERT: F 269 MET cc_start: 0.7995 (mpp) cc_final: 0.7696 (mmm) REVERT: F 299 MET cc_start: 0.8096 (ptm) cc_final: 0.7037 (ptp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0622 time to fit residues: 3.9512 Evaluate side-chains 42 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 64 optimal weight: 20.0000 chunk 180 optimal weight: 0.0030 chunk 79 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 0.0570 chunk 18 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 overall best weight: 2.6114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.070449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063840 restraints weight = 15423.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065136 restraints weight = 9665.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066150 restraints weight = 6639.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066891 restraints weight = 4844.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067390 restraints weight = 3689.439| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.7089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15120 Z= 0.134 Angle : 0.812 8.786 20515 Z= 0.405 Chirality : 0.045 0.181 2275 Planarity : 0.005 0.045 2630 Dihedral : 5.817 36.694 2095 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.92 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 1865 helix: -0.01 (0.20), residues: 630 sheet: -0.65 (0.34), residues: 265 loop : -1.79 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 147 TYR 0.012 0.001 TYR H 166 PHE 0.008 0.001 PHE E 31 TRP 0.022 0.002 TRP H 79 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15120) covalent geometry : angle 0.81228 / 0.41 (20515) hydrogen bonds : bond 0.03625 / 2.39 ( 419) hydrogen bonds : angle 5.79966 / 4.17 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6652 (mmp) cc_final: 0.4007 (mtm) REVERT: F 66 THR cc_start: 0.7676 (m) cc_final: 0.7406 (t) REVERT: F 67 LEU cc_start: 0.8900 (mp) cc_final: 0.8614 (mp) REVERT: F 184 ASP cc_start: 0.8116 (p0) cc_final: 0.7539 (t70) REVERT: F 211 ASP cc_start: 0.7899 (p0) cc_final: 0.6983 (t0) REVERT: F 257 CYS cc_start: 0.8778 (p) cc_final: 0.8559 (m) REVERT: F 269 MET cc_start: 0.7937 (mpp) cc_final: 0.7636 (mmm) REVERT: F 299 MET cc_start: 0.8260 (ptm) cc_final: 0.7245 (ptp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0549 time to fit residues: 3.6604 Evaluate side-chains 43 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 69 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 56 optimal weight: 0.0770 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 165 optimal weight: 0.3980 chunk 160 optimal weight: 0.0970 chunk 67 optimal weight: 0.0270 chunk 126 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066626 restraints weight = 15528.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068006 restraints weight = 10038.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069058 restraints weight = 7012.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069771 restraints weight = 5175.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070339 restraints weight = 4034.280| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.7593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15120 Z= 0.138 Angle : 0.811 8.083 20515 Z= 0.402 Chirality : 0.045 0.155 2275 Planarity : 0.005 0.044 2630 Dihedral : 5.565 35.635 2095 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.38 % Favored : 89.54 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 1865 helix: -0.38 (0.20), residues: 655 sheet: -0.15 (0.33), residues: 290 loop : -1.76 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 116 TYR 0.011 0.001 TYR H 306 PHE 0.007 0.001 PHE D 124 TRP 0.027 0.002 TRP H 79 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (15120) covalent geometry : angle 0.81056 / 0.40 (20515) hydrogen bonds : bond 0.03705 / 2.40 ( 419) hydrogen bonds : angle 5.77674 / 4.13 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 66 THR cc_start: 0.7549 (m) cc_final: 0.7296 (t) REVERT: F 67 LEU cc_start: 0.8788 (mp) cc_final: 0.8512 (mp) REVERT: F 82 MET cc_start: 0.6364 (ttm) cc_final: 0.5532 (ttm) REVERT: F 184 ASP cc_start: 0.8109 (p0) cc_final: 0.7572 (t70) REVERT: F 196 ARG cc_start: 0.8252 (mmt180) cc_final: 0.7577 (mmt90) REVERT: F 211 ASP cc_start: 0.7853 (p0) cc_final: 0.6812 (t0) REVERT: F 269 MET cc_start: 0.7949 (mpp) cc_final: 0.7624 (mmm) REVERT: F 316 GLU cc_start: 0.8756 (mm-30) cc_final: 0.7623 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0611 time to fit residues: 4.2975 Evaluate side-chains 40 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 40 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 68 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.064236 restraints weight = 15665.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065610 restraints weight = 9871.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066728 restraints weight = 6787.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067469 restraints weight = 4905.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068032 restraints weight = 3724.226| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15120 Z= 0.152 Angle : 0.824 7.341 20515 Z= 0.410 Chirality : 0.045 0.152 2275 Planarity : 0.005 0.043 2630 Dihedral : 5.597 31.283 2095 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.19 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.19), residues: 1865 helix: -0.16 (0.21), residues: 625 sheet: -0.43 (0.32), residues: 305 loop : -1.77 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 147 TYR 0.011 0.001 TYR E 166 PHE 0.010 0.001 PHE E 262 TRP 0.051 0.004 TRP H 86 HIS 0.005 0.001 HIS E 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15120) covalent geometry : angle 0.82385 / 0.41 (20515) hydrogen bonds : bond 0.03767 / 2.49 ( 419) hydrogen bonds : angle 5.82003 / 4.14 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 66 THR cc_start: 0.7461 (m) cc_final: 0.7189 (t) REVERT: F 67 LEU cc_start: 0.8961 (mp) cc_final: 0.8651 (mp) REVERT: F 184 ASP cc_start: 0.8059 (p0) cc_final: 0.7618 (t70) REVERT: F 211 ASP cc_start: 0.7895 (p0) cc_final: 0.6832 (t0) REVERT: F 257 CYS cc_start: 0.8963 (m) cc_final: 0.8733 (m) REVERT: F 269 MET cc_start: 0.8050 (mpp) cc_final: 0.7589 (mmp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0541 time to fit residues: 3.5490 Evaluate side-chains 41 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 165 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.071821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065942 restraints weight = 16753.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067028 restraints weight = 10828.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067969 restraints weight = 7621.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068581 restraints weight = 5620.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.068927 restraints weight = 4355.084| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15120 Z= 0.141 Angle : 0.819 14.168 20515 Z= 0.414 Chirality : 0.045 0.154 2275 Planarity : 0.005 0.048 2630 Dihedral : 5.518 33.841 2095 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.26 % Favored : 87.94 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.19), residues: 1865 helix: -0.50 (0.20), residues: 655 sheet: -0.44 (0.32), residues: 305 loop : -1.75 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 210 TYR 0.010 0.001 TYR G 166 PHE 0.011 0.001 PHE H 262 TRP 0.047 0.004 TRP H 86 HIS 0.004 0.001 HIS E 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15120) covalent geometry : angle 0.81885 / 0.41 (20515) hydrogen bonds : bond 0.03698 / 2.45 ( 419) hydrogen bonds : angle 5.83551 / 4.15 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 66 THR cc_start: 0.7623 (m) cc_final: 0.7355 (t) REVERT: F 67 LEU cc_start: 0.8930 (mp) cc_final: 0.8623 (mp) REVERT: F 104 LEU cc_start: 0.8448 (tp) cc_final: 0.8244 (tp) REVERT: F 184 ASP cc_start: 0.8184 (p0) cc_final: 0.7666 (t70) REVERT: F 196 ARG cc_start: 0.8243 (mmt180) cc_final: 0.7719 (mmt90) REVERT: F 257 CYS cc_start: 0.9051 (m) cc_final: 0.8818 (m) REVERT: F 269 MET cc_start: 0.7935 (mpp) cc_final: 0.7567 (mmm) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0390 time to fit residues: 2.5839 Evaluate side-chains 40 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 31 optimal weight: 9.9990 chunk 72 optimal weight: 0.0270 chunk 105 optimal weight: 9.9990 chunk 121 optimal weight: 0.0570 chunk 138 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 174 optimal weight: 0.0030 chunk 110 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 overall best weight: 2.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064408 restraints weight = 15876.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065652 restraints weight = 10139.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066646 restraints weight = 7071.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067410 restraints weight = 5236.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067915 restraints weight = 4034.762| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.8067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15120 Z= 0.133 Angle : 0.818 10.179 20515 Z= 0.404 Chirality : 0.045 0.163 2275 Planarity : 0.005 0.047 2630 Dihedral : 5.427 33.226 2095 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.53 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1865 helix: -0.38 (0.21), residues: 625 sheet: -0.53 (0.31), residues: 305 loop : -1.76 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 116 TYR 0.009 0.001 TYR F 166 PHE 0.009 0.001 PHE D 200 TRP 0.045 0.004 TRP D 86 HIS 0.002 0.001 HIS G 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15120) covalent geometry : angle 0.81780 / 0.40 (20515) hydrogen bonds : bond 0.03641 / 2.41 ( 419) hydrogen bonds : angle 5.81921 / 4.14 ( 1185) =============================================================================== Job complete usr+sys time: 1210.52 seconds wall clock time: 22 minutes 20.72 seconds (1340.72 seconds total)