Starting phenix.real_space_refine on Thu Sep 18 06:00:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j8i_6179/09_2025/3j8i_6179.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j8i_6179/09_2025/3j8i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2025/3j8i_6179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2025/3j8i_6179.map" model { file = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2025/3j8i_6179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j8i_6179/09_2025/3j8i_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.65, per 1000 atoms: 0.25 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: 1.33 Conformation dependent library (CDL) restraints added in 694.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.45 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: 2.89 Time building geometry restraints manager: 1.75 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: 0.310 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 aren 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 covalent geometry : bond 0.01773 (15120) covalent geometry : angle 1.66809 (20515) hydrogen bonds : bond 0.29858 ( 419) hydrogen bonds : angle 10.71833 ( 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: 0.0705 time to fit residues: 8.0687 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 : 0.114 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: F 59 GLN F 87 HIS ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 162 ASN F 296 ASN F 314 GLN F 371 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062366 restraints weight = 15121.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063811 restraints weight = 9139.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.064964 restraints weight = 6156.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065669 restraints weight = 4418.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066191 restraints weight = 3430.287| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4584 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 : 24.14 Ramachandran Plot: Outliers : 1.88 % Allowed : 10.72 % Favored : 87.40 % Rotamer: Outliers : 0.63 % Allowed : 7.86 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (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 covalent geometry : bond 0.00367 (15120) covalent geometry : angle 0.94252 (20515) hydrogen bonds : bond 0.05566 ( 419) hydrogen bonds : angle 6.22046 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 66 THR cc_start: 0.7601 (m) cc_final: 0.7295 (t) REVERT: F 67 LEU cc_start: 0.9028 (mp) cc_final: 0.8574 (mp) REVERT: F 116 ARG cc_start: 0.6759 (mtp180) cc_final: 0.6482 (mtp-110) REVERT: F 134 VAL cc_start: 0.8588 (t) cc_final: 0.7928 (t) REVERT: F 147 ARG cc_start: 0.7355 (mpp-170) cc_final: 0.6758 (mpp-170) REVERT: F 184 ASP cc_start: 0.8380 (p0) cc_final: 0.7847 (t70) REVERT: F 211 ASP cc_start: 0.7896 (p0) cc_final: 0.6139 (t0) REVERT: F 223 PHE cc_start: 0.7798 (t80) cc_final: 0.7587 (t80) REVERT: F 227 MET cc_start: 0.7920 (ttm) cc_final: 0.7689 (ttm) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.0681 time to fit residues: 5.8990 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 : 0.177 ------------------------------------------------------------------------------- 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: 20.0000 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 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: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN F 73 HIS ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** 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 = 0.3258 r_free = 0.3258 target = 0.067660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061778 restraints weight = 16073.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062927 restraints weight = 10128.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063776 restraints weight = 7008.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.064417 restraints weight = 5180.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.064760 restraints weight = 4020.276| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15120 Z= 0.180 Angle : 0.837 7.907 20515 Z= 0.420 Chirality : 0.045 0.160 2275 Planarity : 0.005 0.048 2630 Dihedral : 7.663 97.132 2095 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.99 % Favored : 87.67 % 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 aren not related in a simple way. whole: -1.90 (0.18), residues: 1865 helix: -0.57 (0.18), residues: 685 sheet: -0.21 (0.37), residues: 230 loop : -2.09 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 254 TYR 0.011 0.001 TYR E 294 PHE 0.018 0.002 PHE G 200 TRP 0.013 0.002 TRP H 79 HIS 0.003 0.001 HIS G 161 Details of bonding type rmsd covalent geometry : bond 0.00373 (15120) covalent geometry : angle 0.83667 (20515) hydrogen bonds : bond 0.04729 ( 419) hydrogen bonds : angle 6.11066 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 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 : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 66 THR cc_start: 0.7756 (m) cc_final: 0.7475 (t) REVERT: F 67 LEU cc_start: 0.8979 (mp) cc_final: 0.8572 (mp) REVERT: F 184 ASP cc_start: 0.8352 (p0) cc_final: 0.7918 (t0) REVERT: F 211 ASP cc_start: 0.7906 (p0) cc_final: 0.6859 (t0) REVERT: F 269 MET cc_start: 0.7211 (mpp) cc_final: 0.6739 (mmp) REVERT: F 296 ASN cc_start: 0.7876 (m-40) cc_final: 0.7362 (m-40) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.0726 time to fit residues: 5.2942 Evaluate side-chains 47 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 181 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.065888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.059682 restraints weight = 14934.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060943 restraints weight = 9172.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061939 restraints weight = 6188.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.062619 restraints weight = 4431.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063130 restraints weight = 3387.372| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15120 Z= 0.180 Angle : 0.840 10.135 20515 Z= 0.422 Chirality : 0.046 0.156 2275 Planarity : 0.006 0.055 2630 Dihedral : 7.074 71.105 2095 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 1.61 % Allowed : 10.72 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.18), residues: 1865 helix: -0.47 (0.18), residues: 680 sheet: -0.57 (0.34), residues: 230 loop : -2.09 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 147 TYR 0.011 0.001 TYR G 362 PHE 0.017 0.002 PHE E 262 TRP 0.016 0.002 TRP E 79 HIS 0.003 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00381 (15120) covalent geometry : angle 0.84015 (20515) hydrogen bonds : bond 0.04261 ( 419) hydrogen bonds : angle 5.88210 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 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 : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.9008 (mp) cc_final: 0.8593 (mp) REVERT: F 105 LEU cc_start: 0.6935 (mp) cc_final: 0.6612 (tp) REVERT: F 211 ASP cc_start: 0.7995 (p0) cc_final: 0.7012 (t0) REVERT: F 217 CYS cc_start: 0.6346 (p) cc_final: 0.5642 (p) REVERT: F 269 MET cc_start: 0.8024 (mpp) cc_final: 0.7815 (mmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0683 time to fit residues: 4.6082 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 : 0.124 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 overall best weight: 7.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** 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 = 0.3254 r_free = 0.3254 target = 0.066337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.061183 restraints weight = 16187.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062366 restraints weight = 10044.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063246 restraints weight = 6684.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063845 restraints weight = 4718.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064213 restraints weight = 3509.552| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15120 Z= 0.178 Angle : 0.813 7.515 20515 Z= 0.413 Chirality : 0.045 0.163 2275 Planarity : 0.005 0.045 2630 Dihedral : 6.592 55.239 2095 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 1.61 % Allowed : 10.99 % Favored : 87.40 % Rotamer: Outliers : 0.31 % Allowed : 3.77 % 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 aren not related in a simple way. whole: -2.21 (0.18), residues: 1865 helix: -0.67 (0.19), residues: 680 sheet: -1.22 (0.32), residues: 260 loop : -2.16 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 147 TYR 0.012 0.001 TYR F 166 PHE 0.012 0.002 PHE E 31 TRP 0.014 0.002 TRP G 79 HIS 0.005 0.001 HIS G 161 Details of bonding type rmsd covalent geometry : bond 0.00378 (15120) covalent geometry : angle 0.81287 (20515) hydrogen bonds : bond 0.04026 ( 419) hydrogen bonds : angle 6.31145 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.7068 (mmp) cc_final: 0.4846 (mtt) REVERT: F 67 LEU cc_start: 0.8882 (mp) cc_final: 0.8417 (tp) REVERT: F 184 ASP cc_start: 0.8160 (p0) cc_final: 0.7513 (t70) REVERT: F 196 ARG cc_start: 0.7895 (mmt180) cc_final: 0.7553 (mmt90) REVERT: F 211 ASP cc_start: 0.7942 (p0) cc_final: 0.6960 (t0) REVERT: F 257 CYS cc_start: 0.8840 (p) cc_final: 0.8484 (m) REVERT: F 269 MET cc_start: 0.7889 (mpp) cc_final: 0.7436 (mmp) REVERT: F 299 MET cc_start: 0.8108 (ptm) cc_final: 0.7862 (ptp) REVERT: F 330 ILE cc_start: 0.7537 (mt) cc_final: 0.7196 (mt) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.0647 time to fit residues: 4.8494 Evaluate side-chains 42 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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: 7.9990 chunk 150 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 99 optimal weight: 0.0010 chunk 168 optimal weight: 20.0000 chunk 1 optimal weight: 0.0870 chunk 125 optimal weight: 0.0970 chunk 137 optimal weight: 0.0070 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 overall best weight: 0.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 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 = 0.3312 r_free = 0.3312 target = 0.069429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063158 restraints weight = 15057.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064538 restraints weight = 9169.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065567 restraints weight = 6113.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066280 restraints weight = 4342.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066753 restraints weight = 3240.418| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.7124 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= 0.137 Angle : 0.834 11.476 20515 Z= 0.420 Chirality : 0.046 0.210 2275 Planarity : 0.006 0.052 2630 Dihedral : 5.964 45.466 2095 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.46 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.18), residues: 1865 helix: -0.65 (0.19), residues: 660 sheet: -0.89 (0.33), residues: 260 loop : -2.12 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 147 TYR 0.010 0.001 TYR H 218 PHE 0.007 0.001 PHE G 31 TRP 0.020 0.002 TRP E 79 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00272 (15120) covalent geometry : angle 0.83400 (20515) hydrogen bonds : bond 0.03720 ( 419) hydrogen bonds : angle 5.90816 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6914 (mmp) cc_final: 0.4672 (mtt) REVERT: F 66 THR cc_start: 0.7651 (m) cc_final: 0.7363 (t) REVERT: F 67 LEU cc_start: 0.8906 (mp) cc_final: 0.8496 (mp) REVERT: F 82 MET cc_start: 0.7431 (ttt) cc_final: 0.6877 (ttm) REVERT: F 132 MET cc_start: 0.5848 (ppp) cc_final: 0.5572 (tmm) REVERT: F 184 ASP cc_start: 0.8077 (p0) cc_final: 0.7553 (t70) REVERT: F 211 ASP cc_start: 0.7949 (p0) cc_final: 0.7099 (t0) REVERT: F 257 CYS cc_start: 0.8750 (p) cc_final: 0.8530 (m) REVERT: F 269 MET cc_start: 0.8056 (mpp) cc_final: 0.7709 (mmm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0506 time to fit residues: 4.1210 Evaluate side-chains 46 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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: 0.1980 chunk 79 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 121 optimal weight: 0.0070 chunk 149 optimal weight: 30.0000 chunk 82 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 39 optimal weight: 0.0040 chunk 18 optimal weight: 9.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 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 = 0.3377 r_free = 0.3377 target = 0.072112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065423 restraints weight = 15418.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066812 restraints weight = 9529.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067859 restraints weight = 6451.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.068489 restraints weight = 4680.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069001 restraints weight = 3632.300| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.7533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15120 Z= 0.137 Angle : 0.813 8.926 20515 Z= 0.408 Chirality : 0.047 0.275 2275 Planarity : 0.006 0.045 2630 Dihedral : 5.631 38.154 2095 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.46 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.18), residues: 1865 helix: -0.52 (0.20), residues: 630 sheet: 0.75 (0.45), residues: 160 loop : -2.12 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 206 TYR 0.011 0.001 TYR E 166 PHE 0.009 0.001 PHE H 200 TRP 0.036 0.004 TRP D 86 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00275 (15120) covalent geometry : angle 0.81284 (20515) hydrogen bonds : bond 0.03518 ( 419) hydrogen bonds : angle 5.75336 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 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 : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6842 (mmp) cc_final: 0.4467 (mtm) REVERT: F 66 THR cc_start: 0.7652 (m) cc_final: 0.7400 (t) REVERT: F 67 LEU cc_start: 0.8878 (mp) cc_final: 0.8527 (mp) REVERT: F 184 ASP cc_start: 0.8003 (p0) cc_final: 0.7558 (t70) REVERT: F 211 ASP cc_start: 0.7989 (p0) cc_final: 0.7206 (t0) REVERT: F 269 MET cc_start: 0.7899 (mpp) cc_final: 0.7582 (mmm) REVERT: F 289 ILE cc_start: 0.6999 (tt) cc_final: 0.6648 (tt) REVERT: F 316 GLU cc_start: 0.8840 (mm-30) cc_final: 0.7446 (tp30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0507 time to fit residues: 3.6263 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 : 0.091 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 0.0970 chunk 10 optimal weight: 0.1980 chunk 84 optimal weight: 0.1980 chunk 165 optimal weight: 2.9990 chunk 160 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 chunk 156 optimal weight: 8.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 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 = 0.3408 r_free = 0.3408 target = 0.073665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.067103 restraints weight = 15486.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068501 restraints weight = 9771.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069524 restraints weight = 6644.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070161 restraints weight = 4820.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070715 restraints weight = 3735.565| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.7884 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= 0.131 Angle : 0.793 8.141 20515 Z= 0.394 Chirality : 0.046 0.247 2275 Planarity : 0.006 0.045 2630 Dihedral : 5.477 35.258 2095 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 1.07 % Allowed : 11.53 % Favored : 87.40 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.18), residues: 1865 helix: -0.66 (0.20), residues: 635 sheet: -0.20 (0.33), residues: 260 loop : -2.14 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 177 TYR 0.010 0.001 TYR E 166 PHE 0.007 0.001 PHE D 124 TRP 0.040 0.004 TRP D 86 HIS 0.002 0.000 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00264 (15120) covalent geometry : angle 0.79251 (20515) hydrogen bonds : bond 0.03470 ( 419) hydrogen bonds : angle 5.59478 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 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: 0 poor density : 57 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.8784 (mp) cc_final: 0.8503 (mp) REVERT: F 132 MET cc_start: 0.5920 (ppp) cc_final: 0.5616 (tmm) REVERT: F 184 ASP cc_start: 0.8062 (p0) cc_final: 0.7462 (t70) REVERT: F 211 ASP cc_start: 0.8056 (p0) cc_final: 0.7146 (t0) REVERT: F 269 MET cc_start: 0.7894 (mpp) cc_final: 0.7432 (mmp) REVERT: F 305 MET cc_start: 0.8039 (mmt) cc_final: 0.7698 (mmp) REVERT: F 316 GLU cc_start: 0.8776 (mm-30) cc_final: 0.7634 (tp30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0506 time to fit residues: 3.7219 Evaluate side-chains 39 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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: 40.0000 chunk 131 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 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 = 0.3342 r_free = 0.3342 target = 0.070325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063861 restraints weight = 16824.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065138 restraints weight = 10774.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066055 restraints weight = 7454.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066718 restraints weight = 5474.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.067187 restraints weight = 4238.107| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15120 Z= 0.152 Angle : 0.785 7.151 20515 Z= 0.395 Chirality : 0.046 0.290 2275 Planarity : 0.005 0.042 2630 Dihedral : 5.483 30.175 2095 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.99 % Favored : 87.94 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.19), residues: 1865 helix: -0.78 (0.20), residues: 660 sheet: 0.32 (0.43), residues: 160 loop : -2.04 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 147 TYR 0.010 0.001 TYR H 166 PHE 0.011 0.001 PHE H 262 TRP 0.038 0.003 TRP E 86 HIS 0.002 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00321 (15120) covalent geometry : angle 0.78540 (20515) hydrogen bonds : bond 0.03876 ( 419) hydrogen bonds : angle 5.78193 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6899 (mmp) cc_final: 0.4321 (mtm) REVERT: F 67 LEU cc_start: 0.8818 (mp) cc_final: 0.8546 (tp) REVERT: F 184 ASP cc_start: 0.8059 (p0) cc_final: 0.7593 (t70) REVERT: F 211 ASP cc_start: 0.8144 (p0) cc_final: 0.7155 (t0) REVERT: F 257 CYS cc_start: 0.8958 (m) cc_final: 0.8720 (m) REVERT: F 269 MET cc_start: 0.7928 (mpp) cc_final: 0.7559 (mmm) REVERT: F 299 MET cc_start: 0.8639 (ptm) cc_final: 0.8190 (ppp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0436 time to fit residues: 2.8807 Evaluate side-chains 37 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 7.9990 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 38 optimal weight: 0.0170 chunk 92 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 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 = 0.3422 r_free = 0.3422 target = 0.073521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.067029 restraints weight = 16630.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068314 restraints weight = 10690.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.069289 restraints weight = 7360.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069929 restraints weight = 5375.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070405 restraints weight = 4164.362| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.8171 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= 0.134 Angle : 0.821 14.430 20515 Z= 0.414 Chirality : 0.047 0.303 2275 Planarity : 0.005 0.045 2630 Dihedral : 5.379 30.765 2095 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.46 % Favored : 88.20 % 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 aren not related in a simple way. whole: -2.21 (0.18), residues: 1865 helix: -1.02 (0.19), residues: 635 sheet: -0.61 (0.32), residues: 260 loop : -2.03 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 206 TYR 0.012 0.001 TYR D 306 PHE 0.007 0.001 PHE D 124 TRP 0.041 0.003 TRP H 86 HIS 0.002 0.000 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00269 (15120) covalent geometry : angle 0.82140 (20515) hydrogen bonds : bond 0.03442 ( 419) hydrogen bonds : angle 5.83312 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.7123 (mmp) cc_final: 0.4814 (mtm) REVERT: F 184 ASP cc_start: 0.8015 (p0) cc_final: 0.7541 (t0) REVERT: F 211 ASP cc_start: 0.7848 (p0) cc_final: 0.6863 (t0) REVERT: F 269 MET cc_start: 0.7894 (mpp) cc_final: 0.7544 (mmm) REVERT: F 316 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7542 (tp30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0422 time to fit residues: 2.8808 Evaluate side-chains 38 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 0.1980 chunk 105 optimal weight: 9.9990 chunk 121 optimal weight: 0.0270 chunk 138 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 136 optimal weight: 0.0050 chunk 174 optimal weight: 9.9990 chunk 110 optimal weight: 0.0000 chunk 33 optimal weight: 10.0000 overall best weight: 1.2458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3423 r_free = 0.3423 target = 0.073735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067306 restraints weight = 16553.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068636 restraints weight = 10616.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069529 restraints weight = 7289.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.070224 restraints weight = 5401.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070719 restraints weight = 4176.686| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.8341 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= 0.129 Angle : 0.795 13.027 20515 Z= 0.399 Chirality : 0.046 0.298 2275 Planarity : 0.005 0.048 2630 Dihedral : 5.358 31.143 2095 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.72 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.19), residues: 1865 helix: -1.00 (0.20), residues: 635 sheet: -0.93 (0.31), residues: 295 loop : -2.02 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 206 TYR 0.006 0.001 TYR E 240 PHE 0.008 0.001 PHE H 262 TRP 0.039 0.003 TRP D 86 HIS 0.001 0.000 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00265 (15120) covalent geometry : angle 0.79511 (20515) hydrogen bonds : bond 0.03302 ( 419) hydrogen bonds : angle 5.87251 ( 1185) =============================================================================== Job complete usr+sys time: 1139.93 seconds wall clock time: 21 minutes 6.51 seconds (1266.51 seconds total)