Starting phenix.real_space_refine on Fri Jun 13 01:28:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j8i_6179/06_2025/3j8i_6179.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j8i_6179/06_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_6179/06_2025/3j8i_6179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j8i_6179/06_2025/3j8i_6179.map" model { file = "/net/cci-nas-00/data/ceres_data/3j8i_6179/06_2025/3j8i_6179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j8i_6179/06_2025/3j8i_6179.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.79, per 1000 atoms: 0.59 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: 4.46 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.60 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: 4.25 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4526 1.34 - 1.48: 4024 1.48 - 1.63: 6385 1.63 - 1.77: 21 1.77 - 1.91: 164 Bond restraints: 15120 Sorted by residual: bond pdb=" C LEU D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.331 1.383 -0.052 7.90e-03 1.60e+04 4.29e+01 bond pdb=" C LEU H 171 " pdb=" N PRO H 172 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.05e+01 bond pdb=" C LEU F 171 " pdb=" N PRO F 172 " ideal model delta sigma weight residual 1.331 1.379 -0.047 7.90e-03 1.60e+04 3.55e+01 bond pdb=" CA ILE E 250 " pdb=" C ILE E 250 " ideal model delta sigma weight residual 1.526 1.474 0.052 9.00e-03 1.23e+04 3.32e+01 bond pdb=" C LEU E 171 " pdb=" N PRO E 172 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.24e+01 ... (remaining 15115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18152 2.36 - 4.72: 1921 4.72 - 7.08: 359 7.08 - 9.44: 54 9.44 - 11.80: 29 Bond angle restraints: 20515 Sorted by residual: angle pdb=" C VAL F 129 " pdb=" N PRO F 130 " pdb=" CA PRO F 130 " ideal model delta sigma weight residual 119.19 126.79 -7.60 1.06e+00 8.90e-01 5.13e+01 angle pdb=" C ALA D 108 " pdb=" N PRO D 109 " pdb=" CA PRO D 109 " ideal model delta sigma weight residual 119.78 127.02 -7.24 1.03e+00 9.43e-01 4.94e+01 angle pdb=" N ALA G 138 " pdb=" CA ALA G 138 " pdb=" C ALA G 138 " ideal model delta sigma weight residual 111.28 118.53 -7.25 1.09e+00 8.42e-01 4.42e+01 angle pdb=" C ALA G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta sigma weight residual 119.78 126.55 -6.77 1.03e+00 9.43e-01 4.32e+01 angle pdb=" N ALA D 138 " pdb=" CA ALA D 138 " pdb=" C ALA D 138 " ideal model delta sigma weight residual 111.36 118.09 -6.73 1.09e+00 8.42e-01 3.81e+01 ... (remaining 20510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8650 35.49 - 70.97: 411 70.97 - 106.46: 34 106.46 - 141.94: 5 141.94 - 177.43: 5 Dihedral angle restraints: 9105 sinusoidal: 3685 harmonic: 5420 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.33 -177.32 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 9102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1407 0.093 - 0.185: 657 0.185 - 0.278: 181 0.278 - 0.370: 24 0.370 - 0.463: 6 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO E 243 " pdb=" N PRO E 243 " pdb=" C PRO E 243 " pdb=" CB PRO E 243 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA PRO F 243 " pdb=" N PRO F 243 " pdb=" C PRO F 243 " pdb=" CB PRO F 243 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CA PRO H 243 " pdb=" N PRO H 243 " pdb=" C PRO H 243 " pdb=" CB PRO H 243 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 2272 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 166 " -0.071 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR D 166 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 166 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 166 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR D 166 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 166 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D 166 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 166 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 166 " 0.061 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR E 166 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR E 166 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 166 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR E 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 166 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 166 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 166 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 166 " -0.060 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR H 166 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR H 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 166 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR H 166 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 166 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR H 166 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR H 166 " -0.027 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 784 2.68 - 3.24: 16908 3.24 - 3.79: 24664 3.79 - 4.35: 32343 4.35 - 4.90: 50125 Nonbonded interactions: 124824 Sorted by model distance: nonbonded pdb=" O SER F 350 " pdb=" N PHE F 352 " model vdw 2.125 3.120 nonbonded pdb=" O TYR H 362 " pdb=" O ALA H 365 " model vdw 2.131 3.040 nonbonded pdb=" O TYR F 362 " pdb=" O ALA F 365 " model vdw 2.140 3.040 nonbonded pdb=" O TYR G 362 " pdb=" O ALA G 365 " model vdw 2.154 3.040 nonbonded pdb=" O SER D 350 " pdb=" N PHE D 352 " model vdw 2.160 3.120 ... (remaining 124819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 34.840 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (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 TRP 0.041 0.009 TRP G 356 HIS 0.004 0.001 HIS E 101 PHE 0.030 0.005 PHE G 375 TYR 0.071 0.009 TYR D 166 ARG 0.012 0.002 ARG E 290 Details of bonding type rmsd hydrogen bonds : bond 0.29858 ( 419) hydrogen bonds : angle 10.71833 ( 1185) covalent geometry : bond 0.01773 (15120) covalent geometry : angle 1.66809 (20515) *********************** 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 105 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 59 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6477 (p0) REVERT: H 31 PHE cc_start: 0.5922 (OUTLIER) cc_final: 0.5189 (p90) REVERT: H 49 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5732 (tm-30) REVERT: H 76 ILE cc_start: 0.8205 (mt) cc_final: 0.7888 (mt) REVERT: H 79 TRP cc_start: 0.8262 (OUTLIER) cc_final: 0.7814 (m100) REVERT: H 82 MET cc_start: 0.8378 (ttt) cc_final: 0.8036 (ttt) REVERT: H 116 ARG cc_start: 0.6902 (mtp180) cc_final: 0.6457 (mtp-110) REVERT: H 147 ARG cc_start: 0.7757 (mpp-170) cc_final: 0.7096 (mpp-170) REVERT: H 160 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7147 (p) REVERT: H 196 ARG cc_start: 0.7452 (mmt180) cc_final: 0.6187 (tpp80) REVERT: H 202 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8436 (t) REVERT: H 223 PHE cc_start: 0.8425 (t80) cc_final: 0.8138 (t80) REVERT: H 227 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8701 (mtp) REVERT: H 259 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: H 276 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8255 (tm-30) REVERT: H 304 THR cc_start: 0.8810 (m) cc_final: 0.8407 (p) REVERT: H 306 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8491 (t80) REVERT: H 313 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8155 (tpp) outliers start: 46 outliers final: 18 residues processed: 98 average time/residue: 0.2276 time to fit residues: 25.9003 Evaluate side-chains 72 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 44 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 107 optimal weight: 0.0010 chunk 168 optimal weight: 20.0000 overall best weight: 1.9888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 296 ASN F 297 ASN F 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061968 restraints weight = 14933.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063429 restraints weight = 9304.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.064506 restraints weight = 6344.960| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15120 Z= 0.182 Angle : 0.939 9.585 20515 Z= 0.473 Chirality : 0.051 0.220 2275 Planarity : 0.007 0.070 2630 Dihedral : 8.944 121.896 2095 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 26.87 Ramachandran Plot: Outliers : 1.88 % Allowed : 10.19 % Favored : 87.94 % Rotamer: Outliers : 1.26 % Allowed : 7.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.18), residues: 1865 helix: -0.50 (0.19), residues: 655 sheet: 0.44 (0.42), residues: 190 loop : -2.10 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP G 86 HIS 0.007 0.002 HIS G 161 PHE 0.009 0.001 PHE E 31 TYR 0.011 0.002 TYR D 294 ARG 0.010 0.001 ARG G 206 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 419) hydrogen bonds : angle 6.66044 ( 1185) covalent geometry : bond 0.00375 (15120) covalent geometry : angle 0.93900 (20515) *********************** 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 79 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.6962 (mtp180) cc_final: 0.6743 (mtp-110) REVERT: F 147 ARG cc_start: 0.7203 (mpp-170) cc_final: 0.6634 (mpp-170) REVERT: F 184 ASP cc_start: 0.8475 (p0) cc_final: 0.7654 (t70) REVERT: F 211 ASP cc_start: 0.7773 (p0) cc_final: 0.6057 (t0) REVERT: F 223 PHE cc_start: 0.7801 (t80) cc_final: 0.7599 (t80) REVERT: F 274 ILE cc_start: 0.8576 (tp) cc_final: 0.8201 (tp) REVERT: F 276 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7873 (tp30) outliers start: 4 outliers final: 0 residues processed: 77 average time/residue: 0.1619 time to fit residues: 14.8359 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 : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 4 optimal weight: 30.0000 chunk 173 optimal weight: 0.1980 chunk 95 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 135 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 133 optimal weight: 0.0770 chunk 178 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.0544 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.068363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.061544 restraints weight = 14192.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062899 restraints weight = 8922.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063920 restraints weight = 6125.409| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5223 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= 0.147 Angle : 0.838 7.737 20515 Z= 0.417 Chirality : 0.047 0.221 2275 Planarity : 0.005 0.043 2630 Dihedral : 7.602 97.019 2095 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.19 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.18), residues: 1865 helix: -0.74 (0.18), residues: 675 sheet: 0.33 (0.38), residues: 215 loop : -2.07 (0.17), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 79 HIS 0.004 0.001 HIS G 161 PHE 0.019 0.002 PHE H 200 TYR 0.011 0.001 TYR E 294 ARG 0.002 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 419) hydrogen bonds : angle 5.89156 ( 1185) covalent geometry : bond 0.00300 (15120) covalent geometry : angle 0.83763 (20515) *********************** 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 61 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 25 ASP cc_start: 0.7715 (m-30) cc_final: 0.7467 (m-30) REVERT: F 67 LEU cc_start: 0.9104 (mp) cc_final: 0.8614 (mp) REVERT: F 184 ASP cc_start: 0.8268 (p0) cc_final: 0.7723 (t0) REVERT: F 211 ASP cc_start: 0.7839 (p0) cc_final: 0.6664 (t0) REVERT: F 276 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7672 (tp30) REVERT: F 296 ASN cc_start: 0.7558 (m-40) cc_final: 0.7306 (m-40) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1689 time to fit residues: 12.3720 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 : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 108 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 19 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 115 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 40.0000 overall best weight: 0.9538 ------------------------------------------------------------------------------- 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 101 HIS ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.064695 restraints weight = 14674.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066065 restraints weight = 8989.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067140 restraints weight = 6116.755| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.6018 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= 0.143 Angle : 0.840 10.121 20515 Z= 0.418 Chirality : 0.046 0.229 2275 Planarity : 0.006 0.057 2630 Dihedral : 6.942 73.297 2095 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.19 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.18), residues: 1865 helix: -0.42 (0.20), residues: 635 sheet: 0.02 (0.36), residues: 230 loop : -1.96 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 79 HIS 0.006 0.001 HIS G 161 PHE 0.015 0.001 PHE D 223 TYR 0.008 0.001 TYR D 169 ARG 0.004 0.001 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 419) hydrogen bonds : angle 6.06199 ( 1185) covalent geometry : bond 0.00289 (15120) covalent geometry : angle 0.83952 (20515) *********************** 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 61 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.8935 (mp) cc_final: 0.8502 (mp) REVERT: F 104 LEU cc_start: 0.8801 (tp) cc_final: 0.8505 (tp) REVERT: F 211 ASP cc_start: 0.7702 (p0) cc_final: 0.6639 (t0) REVERT: F 217 CYS cc_start: 0.5282 (p) cc_final: 0.4917 (p) REVERT: F 274 ILE cc_start: 0.8451 (tp) cc_final: 0.8023 (tp) REVERT: F 276 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7663 (tp30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1598 time to fit residues: 12.0272 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 : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 95 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 171 optimal weight: 30.0000 chunk 181 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 115 ASN F 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063836 restraints weight = 14920.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065171 restraints weight = 9028.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066143 restraints weight = 6007.985| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15120 Z= 0.145 Angle : 0.808 8.244 20515 Z= 0.404 Chirality : 0.047 0.274 2275 Planarity : 0.005 0.041 2630 Dihedral : 6.380 53.353 2095 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.92 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.18), residues: 1865 helix: -0.53 (0.19), residues: 650 sheet: 0.13 (0.37), residues: 225 loop : -1.89 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 79 HIS 0.007 0.001 HIS G 161 PHE 0.008 0.001 PHE H 31 TYR 0.010 0.001 TYR F 169 ARG 0.011 0.001 ARG H 256 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 419) hydrogen bonds : angle 5.81330 ( 1185) covalent geometry : bond 0.00305 (15120) covalent geometry : angle 0.80828 (20515) *********************** 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 50 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.8943 (mp) cc_final: 0.8555 (mp) REVERT: F 104 LEU cc_start: 0.8787 (tp) cc_final: 0.8407 (tp) REVERT: F 105 LEU cc_start: 0.8229 (tp) cc_final: 0.7979 (mp) REVERT: F 211 ASP cc_start: 0.7818 (p0) cc_final: 0.6856 (t0) REVERT: F 274 ILE cc_start: 0.8375 (tp) cc_final: 0.8036 (tp) REVERT: F 276 GLU cc_start: 0.8608 (mt-10) cc_final: 0.7757 (tp30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1501 time to fit residues: 9.2872 Evaluate side-chains 42 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 92 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 57 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 32 optimal weight: 0.0170 chunk 121 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 overall best weight: 2.3022 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064882 restraints weight = 15550.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066268 restraints weight = 9359.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067284 restraints weight = 6203.718| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.6821 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= 0.133 Angle : 0.792 9.658 20515 Z= 0.396 Chirality : 0.045 0.185 2275 Planarity : 0.005 0.043 2630 Dihedral : 5.974 39.067 2095 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.19 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.19), residues: 1865 helix: -0.55 (0.19), residues: 650 sheet: 0.36 (0.42), residues: 180 loop : -1.73 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 86 HIS 0.008 0.001 HIS G 161 PHE 0.006 0.001 PHE F 31 TYR 0.011 0.001 TYR H 169 ARG 0.005 0.001 ARG E 147 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 419) hydrogen bonds : angle 5.88919 ( 1185) covalent geometry : bond 0.00274 (15120) covalent geometry : angle 0.79164 (20515) *********************** 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 57 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.8876 (mp) cc_final: 0.8513 (mp) REVERT: F 104 LEU cc_start: 0.8708 (tp) cc_final: 0.8483 (tp) REVERT: F 184 ASP cc_start: 0.8246 (p0) cc_final: 0.7403 (t70) REVERT: F 211 ASP cc_start: 0.7984 (p0) cc_final: 0.6941 (t0) REVERT: F 274 ILE cc_start: 0.8437 (tp) cc_final: 0.8175 (tp) REVERT: F 276 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7722 (tp30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1552 time to fit residues: 10.8162 Evaluate side-chains 43 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 22 optimal weight: 0.0050 chunk 88 optimal weight: 0.0010 chunk 39 optimal weight: 30.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.072028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064864 restraints weight = 16313.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066226 restraints weight = 10343.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067260 restraints weight = 7189.633| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15120 Z= 0.135 Angle : 0.811 12.076 20515 Z= 0.411 Chirality : 0.046 0.174 2275 Planarity : 0.005 0.041 2630 Dihedral : 5.856 36.131 2095 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.12 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 1865 helix: -0.48 (0.20), residues: 650 sheet: -0.29 (0.35), residues: 245 loop : -1.86 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 86 HIS 0.003 0.001 HIS H 161 PHE 0.007 0.001 PHE G 127 TYR 0.011 0.001 TYR F 169 ARG 0.005 0.001 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 419) hydrogen bonds : angle 5.78327 ( 1185) covalent geometry : bond 0.00286 (15120) covalent geometry : angle 0.81140 (20515) *********************** 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 56 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.9044 (mp) cc_final: 0.8675 (mp) REVERT: F 104 LEU cc_start: 0.8703 (tp) cc_final: 0.8502 (tp) REVERT: F 184 ASP cc_start: 0.8233 (p0) cc_final: 0.7520 (t0) REVERT: F 198 TYR cc_start: 0.7717 (m-80) cc_final: 0.7511 (m-10) REVERT: F 211 ASP cc_start: 0.7964 (p0) cc_final: 0.6820 (t70) REVERT: F 274 ILE cc_start: 0.8432 (tp) cc_final: 0.8230 (tp) REVERT: F 276 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7664 (tp30) REVERT: F 316 GLU cc_start: 0.8725 (mm-30) cc_final: 0.7310 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1508 time to fit residues: 10.3110 Evaluate side-chains 43 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 133 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 25 optimal weight: 0.0370 chunk 177 optimal weight: 10.0000 chunk 96 optimal weight: 0.0770 chunk 4 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 chunk 158 optimal weight: 8.9990 overall best weight: 1.4318 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066067 restraints weight = 16077.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067333 restraints weight = 10271.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068366 restraints weight = 7202.473| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.7547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15120 Z= 0.130 Angle : 0.797 10.133 20515 Z= 0.398 Chirality : 0.048 0.288 2275 Planarity : 0.005 0.042 2630 Dihedral : 5.690 34.863 2095 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.53 % Favored : 87.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.19), residues: 1865 helix: -0.51 (0.20), residues: 650 sheet: -0.05 (0.35), residues: 255 loop : -1.88 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 86 HIS 0.008 0.001 HIS G 161 PHE 0.005 0.001 PHE E 31 TYR 0.011 0.001 TYR H 169 ARG 0.005 0.000 ARG E 147 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 419) hydrogen bonds : angle 5.77378 ( 1185) covalent geometry : bond 0.00268 (15120) covalent geometry : angle 0.79672 (20515) *********************** 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 55 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.8973 (mp) cc_final: 0.8623 (mp) REVERT: F 132 MET cc_start: 0.6328 (tmm) cc_final: 0.5908 (tmm) REVERT: F 184 ASP cc_start: 0.8180 (p0) cc_final: 0.7479 (t70) REVERT: F 211 ASP cc_start: 0.7705 (p0) cc_final: 0.6673 (t0) REVERT: F 274 ILE cc_start: 0.8465 (tp) cc_final: 0.8145 (tp) REVERT: F 276 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7621 (tp30) REVERT: F 316 GLU cc_start: 0.8622 (mm-30) cc_final: 0.7332 (tp30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1490 time to fit residues: 10.1642 Evaluate side-chains 42 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 chunk 29 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 28 optimal weight: 0.0040 chunk 50 optimal weight: 0.0020 chunk 43 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 overall best weight: 1.0880 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.076311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.069959 restraints weight = 16439.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071105 restraints weight = 10804.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071983 restraints weight = 7688.046| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.7886 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= 0.125 Angle : 0.789 9.424 20515 Z= 0.394 Chirality : 0.047 0.291 2275 Planarity : 0.005 0.040 2630 Dihedral : 5.509 32.680 2095 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.53 % Favored : 87.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.19), residues: 1865 helix: -0.63 (0.19), residues: 650 sheet: -0.38 (0.34), residues: 230 loop : -1.89 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 86 HIS 0.004 0.001 HIS G 161 PHE 0.008 0.001 PHE H 375 TYR 0.012 0.001 TYR E 198 ARG 0.002 0.000 ARG G 147 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 419) hydrogen bonds : angle 5.71450 ( 1185) covalent geometry : bond 0.00265 (15120) covalent geometry : angle 0.78922 (20515) *********************** 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 52 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.8973 (mp) cc_final: 0.8558 (mp) REVERT: F 176 MET cc_start: 0.8635 (tmm) cc_final: 0.7424 (tmm) REVERT: F 184 ASP cc_start: 0.8095 (p0) cc_final: 0.7585 (t0) REVERT: F 196 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7844 (mmt90) REVERT: F 274 ILE cc_start: 0.8512 (tp) cc_final: 0.8270 (tp) REVERT: F 276 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7619 (tm-30) REVERT: F 316 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7184 (tp30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2063 time to fit residues: 13.5910 Evaluate side-chains 40 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 51 optimal weight: 0.0770 chunk 64 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 28 optimal weight: 0.0170 chunk 100 optimal weight: 0.0670 chunk 44 optimal weight: 6.9990 chunk 90 optimal weight: 0.0060 chunk 171 optimal weight: 8.9990 chunk 113 optimal weight: 0.2980 chunk 33 optimal weight: 8.9990 overall best weight: 0.0930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072270 restraints weight = 16101.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073453 restraints weight = 10912.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074186 restraints weight = 7862.429| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.8344 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= 0.129 Angle : 0.819 11.269 20515 Z= 0.405 Chirality : 0.048 0.318 2275 Planarity : 0.005 0.041 2630 Dihedral : 5.373 31.233 2095 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.80 % Favored : 87.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 1865 helix: -0.47 (0.20), residues: 615 sheet: -0.75 (0.30), residues: 270 loop : -1.84 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 86 HIS 0.006 0.001 HIS H 161 PHE 0.005 0.001 PHE H 375 TYR 0.012 0.001 TYR H 198 ARG 0.003 0.000 ARG F 290 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 419) hydrogen bonds : angle 5.77564 ( 1185) covalent geometry : bond 0.00266 (15120) covalent geometry : angle 0.81875 (20515) ********************** 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 53 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.8992 (mp) cc_final: 0.8597 (mp) REVERT: F 132 MET cc_start: 0.5733 (tmm) cc_final: 0.5428 (tmm) REVERT: F 176 MET cc_start: 0.8480 (tmm) cc_final: 0.6941 (tmm) REVERT: F 184 ASP cc_start: 0.8119 (p0) cc_final: 0.7520 (t0) REVERT: F 196 ARG cc_start: 0.8246 (mmt180) cc_final: 0.7556 (mmt90) REVERT: F 276 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7571 (tm-30) REVERT: F 316 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7256 (tp30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2190 time to fit residues: 14.5065 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 : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 chunk 135 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 99 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 78 optimal weight: 0.7980 overall best weight: 4.3986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067711 restraints weight = 16484.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068833 restraints weight = 10743.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069686 restraints weight = 7662.558| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.8279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15120 Z= 0.149 Angle : 0.833 11.622 20515 Z= 0.411 Chirality : 0.046 0.279 2275 Planarity : 0.005 0.038 2630 Dihedral : 5.482 30.968 2095 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.99 % Favored : 88.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.19), residues: 1865 helix: -0.31 (0.20), residues: 650 sheet: -0.88 (0.28), residues: 270 loop : -1.81 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 86 HIS 0.003 0.001 HIS H 161 PHE 0.008 0.001 PHE H 31 TYR 0.010 0.001 TYR G 198 ARG 0.005 0.001 ARG E 290 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 419) hydrogen bonds : angle 5.73324 ( 1185) covalent geometry : bond 0.00324 (15120) covalent geometry : angle 0.83291 (20515) =============================================================================== Job complete usr+sys time: 2795.38 seconds wall clock time: 52 minutes 13.15 seconds (3133.15 seconds total)