Starting phenix.real_space_refine on Fri Sep 27 00:48:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/09_2024/3j8i_6179.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/09_2024/3j8i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/09_2024/3j8i_6179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/09_2024/3j8i_6179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/09_2024/3j8i_6179.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/09_2024/3j8i_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.49, per 1000 atoms: 0.57 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: 4.22 Conformation dependent library (CDL) restraints added in 2.1 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: 1.66 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: 4.40 Time building geometry restraints manager: 4.70 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: 0.00 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 34.710 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.100 ------------------------------------------------------------------------------- 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= 1.171 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 *********************** 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 fitting. rotamer outliers: 46 poor density : 60 time to evaluate : 0.315 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: 0.1560 time to fit residues: 17.8711 Evaluate side-chains 60 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 0.2980 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 0.0020 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 overall best weight: 3.2594 ------------------------------------------------------------------------------- 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 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 296 ASN F 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4362 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= 0.257 Angle : 0.938 9.384 20515 Z= 0.470 Chirality : 0.049 0.195 2275 Planarity : 0.006 0.039 2630 Dihedral : 8.747 119.424 2095 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 1.88 % Allowed : 10.46 % Favored : 87.67 % 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 (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: -1.56 (0.19), residues: 1865 helix: 0.09 (0.20), residues: 645 sheet: 0.11 (0.38), residues: 220 loop : -2.15 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 79 HIS 0.010 0.002 HIS G 40 PHE 0.010 0.002 PHE H 255 TYR 0.019 0.002 TYR F 169 ARG 0.005 0.001 ARG D 254 *********************** 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 71 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 ASP cc_start: 0.8409 (m-30) cc_final: 0.7968 (p0) REVERT: F 116 ARG cc_start: 0.7024 (mtp180) cc_final: 0.6782 (mtp-110) REVERT: F 134 VAL cc_start: 0.8997 (t) cc_final: 0.8492 (t) REVERT: F 147 ARG cc_start: 0.7831 (mpp-170) cc_final: 0.7167 (mpp-170) REVERT: F 184 ASP cc_start: 0.9217 (p0) cc_final: 0.8599 (t70) REVERT: F 211 ASP cc_start: 0.8292 (p0) cc_final: 0.7392 (p0) REVERT: F 305 MET cc_start: 0.8748 (tpp) cc_final: 0.8522 (tpp) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.1631 time to fit residues: 13.7281 Evaluate side-chains 49 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 181 optimal weight: 8.9990 chunk 149 optimal weight: 0.0980 chunk 166 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 137 GLN F 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5378 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= 0.197 Angle : 0.826 7.939 20515 Z= 0.411 Chirality : 0.047 0.236 2275 Planarity : 0.005 0.044 2630 Dihedral : 7.540 95.073 2095 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.99 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % 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: -1.94 (0.18), residues: 1865 helix: -0.58 (0.19), residues: 680 sheet: -0.13 (0.37), residues: 230 loop : -2.17 (0.17), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 79 HIS 0.010 0.002 HIS E 73 PHE 0.020 0.002 PHE H 200 TYR 0.012 0.001 TYR E 218 ARG 0.003 0.000 ARG F 254 *********************** 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 fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.9296 (mp) cc_final: 0.9052 (mp) REVERT: F 211 ASP cc_start: 0.8290 (p0) cc_final: 0.7129 (t0) REVERT: F 217 CYS cc_start: 0.7156 (p) cc_final: 0.5835 (p) REVERT: F 296 ASN cc_start: 0.8193 (m-40) cc_final: 0.7927 (m-40) REVERT: F 305 MET cc_start: 0.8657 (tpp) cc_final: 0.8316 (mpp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1763 time to fit residues: 12.6509 Evaluate side-chains 44 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 7.9990 chunk 126 optimal weight: 0.0980 chunk 87 optimal weight: 0.0050 chunk 18 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 113 optimal weight: 0.0060 chunk 168 optimal weight: 20.0000 chunk 178 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 overall best weight: 0.3210 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6210 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= 0.178 Angle : 0.831 9.771 20515 Z= 0.412 Chirality : 0.046 0.156 2275 Planarity : 0.006 0.064 2630 Dihedral : 6.877 74.292 2095 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.99 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.99 (0.17), residues: 1865 helix: -0.62 (0.19), residues: 620 sheet: 0.02 (0.38), residues: 210 loop : -2.13 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 340 HIS 0.006 0.001 HIS E 73 PHE 0.008 0.001 PHE F 262 TYR 0.010 0.001 TYR F 218 ARG 0.007 0.001 ARG G 147 *********************** 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 57 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 67 LEU cc_start: 0.9260 (mp) cc_final: 0.9048 (mp) REVERT: F 132 MET cc_start: 0.6045 (ppp) cc_final: 0.5803 (tmm) REVERT: F 211 ASP cc_start: 0.8285 (p0) cc_final: 0.7179 (t0) REVERT: F 217 CYS cc_start: 0.7026 (p) cc_final: 0.5969 (p) REVERT: F 269 MET cc_start: 0.8002 (mpp) cc_final: 0.7514 (mmm) REVERT: F 284 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7796 (tttt) REVERT: F 305 MET cc_start: 0.8440 (tpp) cc_final: 0.8216 (mpp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1034 time to fit residues: 7.7118 Evaluate side-chains 43 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 73 optimal weight: 0.0170 chunk 152 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 overall best weight: 3.5224 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.6525 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= 0.194 Angle : 0.808 7.594 20515 Z= 0.406 Chirality : 0.045 0.155 2275 Planarity : 0.005 0.043 2630 Dihedral : 6.277 50.323 2095 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.19 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -1.76 (0.18), residues: 1865 helix: -0.53 (0.19), residues: 630 sheet: 0.22 (0.39), residues: 210 loop : -1.94 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 79 HIS 0.005 0.001 HIS H 73 PHE 0.008 0.001 PHE H 262 TYR 0.011 0.001 TYR H 166 ARG 0.004 0.001 ARG G 256 *********************** 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 56 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6397 (mmm) cc_final: 0.4258 (mtm) REVERT: F 67 LEU cc_start: 0.9293 (mp) cc_final: 0.9069 (mp) REVERT: F 104 LEU cc_start: 0.9087 (tp) cc_final: 0.8884 (tp) REVERT: F 184 ASP cc_start: 0.9034 (p0) cc_final: 0.8322 (t70) REVERT: F 211 ASP cc_start: 0.8404 (p0) cc_final: 0.7394 (t0) REVERT: F 257 CYS cc_start: 0.9198 (p) cc_final: 0.8990 (m) REVERT: F 269 MET cc_start: 0.8027 (mpp) cc_final: 0.7323 (mmp) REVERT: F 305 MET cc_start: 0.8440 (tpp) cc_final: 0.8124 (mpp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1318 time to fit residues: 9.3022 Evaluate side-chains 42 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 0.0270 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 148 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15120 Z= 0.172 Angle : 0.798 11.449 20515 Z= 0.398 Chirality : 0.045 0.212 2275 Planarity : 0.005 0.047 2630 Dihedral : 5.821 44.924 2095 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.92 % Favored : 89.28 % 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 (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: -1.74 (0.18), residues: 1865 helix: -0.56 (0.19), residues: 635 sheet: 0.12 (0.35), residues: 230 loop : -1.90 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 86 HIS 0.003 0.001 HIS D 87 PHE 0.007 0.001 PHE D 31 TYR 0.009 0.001 TYR G 166 ARG 0.004 0.001 ARG F 116 *********************** 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 52 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 132 MET cc_start: 0.6265 (ppp) cc_final: 0.5822 (tmm) REVERT: F 184 ASP cc_start: 0.9025 (p0) cc_final: 0.8271 (t70) REVERT: F 211 ASP cc_start: 0.8410 (p0) cc_final: 0.7380 (t0) REVERT: F 269 MET cc_start: 0.8058 (mpp) cc_final: 0.7553 (mmm) REVERT: F 283 MET cc_start: 0.9001 (mmm) cc_final: 0.8752 (mmm) REVERT: F 299 MET cc_start: 0.8754 (ptm) cc_final: 0.8323 (ptm) REVERT: F 316 GLU cc_start: 0.9024 (mm-30) cc_final: 0.7998 (tp30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1224 time to fit residues: 8.1515 Evaluate side-chains 43 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 101 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 99 optimal weight: 0.1980 chunk 178 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 82 optimal weight: 0.0570 chunk 110 optimal weight: 0.0270 overall best weight: 1.5558 ------------------------------------------------------------------------------- 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.7303 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= 0.166 Angle : 0.784 8.846 20515 Z= 0.394 Chirality : 0.044 0.164 2275 Planarity : 0.005 0.043 2630 Dihedral : 5.624 38.145 2095 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.46 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.80 (0.19), residues: 1865 helix: -0.48 (0.20), residues: 630 sheet: 0.90 (0.48), residues: 130 loop : -1.98 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP E 86 HIS 0.004 0.001 HIS G 161 PHE 0.008 0.001 PHE E 31 TYR 0.009 0.001 TYR G 166 ARG 0.005 0.001 ARG E 290 *********************** 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 51 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 184 ASP cc_start: 0.9018 (p0) cc_final: 0.8315 (t70) REVERT: F 211 ASP cc_start: 0.8403 (p0) cc_final: 0.7383 (t0) REVERT: F 269 MET cc_start: 0.8127 (mpp) cc_final: 0.7383 (mmp) REVERT: F 284 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7858 (tttt) REVERT: F 316 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8053 (tp30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1333 time to fit residues: 8.5353 Evaluate side-chains 41 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 53 optimal weight: 0.0030 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 30.0000 chunk 113 optimal weight: 0.0370 chunk 121 optimal weight: 0.0870 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 162 optimal weight: 0.0010 overall best weight: 0.2052 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.7797 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= 0.168 Angle : 0.769 8.452 20515 Z= 0.383 Chirality : 0.045 0.154 2275 Planarity : 0.005 0.046 2630 Dihedral : 5.434 38.419 2095 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.99 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.64 (0.19), residues: 1865 helix: -0.34 (0.21), residues: 635 sheet: 1.23 (0.45), residues: 160 loop : -2.02 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 86 HIS 0.002 0.000 HIS D 87 PHE 0.008 0.001 PHE D 31 TYR 0.026 0.001 TYR H 294 ARG 0.003 0.000 ARG D 147 *********************** 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 52 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 111 ASN cc_start: 0.4613 (t0) cc_final: 0.3992 (t0) REVERT: F 132 MET cc_start: 0.6168 (ppp) cc_final: 0.5755 (tmm) REVERT: F 184 ASP cc_start: 0.8994 (p0) cc_final: 0.8285 (t0) REVERT: F 211 ASP cc_start: 0.8478 (p0) cc_final: 0.7470 (t0) REVERT: F 269 MET cc_start: 0.8102 (mpp) cc_final: 0.7350 (mmp) REVERT: F 284 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7851 (tttt) REVERT: F 316 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8045 (tp30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1188 time to fit residues: 7.9624 Evaluate side-chains 38 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 0.0000 chunk 157 optimal weight: 0.8980 chunk 165 optimal weight: 0.0370 chunk 109 optimal weight: 9.9990 overall best weight: 1.5866 ------------------------------------------------------------------------------- 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 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.8046 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= 0.175 Angle : 0.776 8.095 20515 Z= 0.385 Chirality : 0.044 0.144 2275 Planarity : 0.005 0.042 2630 Dihedral : 5.414 35.099 2095 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.72 % Favored : 88.74 % 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: -1.87 (0.19), residues: 1865 helix: -0.59 (0.20), residues: 645 sheet: 1.10 (0.48), residues: 135 loop : -2.05 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 86 HIS 0.002 0.001 HIS E 73 PHE 0.008 0.001 PHE E 31 TYR 0.011 0.001 TYR G 294 ARG 0.007 0.001 ARG D 147 *********************** 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 fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 111 ASN cc_start: 0.4410 (t0) cc_final: 0.3879 (t0) REVERT: F 132 MET cc_start: 0.6135 (ppp) cc_final: 0.5661 (tmm) REVERT: F 184 ASP cc_start: 0.8958 (p0) cc_final: 0.8286 (t0) REVERT: F 211 ASP cc_start: 0.8517 (p0) cc_final: 0.7415 (t0) REVERT: F 284 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7845 (tttt) REVERT: F 299 MET cc_start: 0.8948 (ppp) cc_final: 0.8730 (ppp) REVERT: F 305 MET cc_start: 0.8349 (mmt) cc_final: 0.8134 (mmt) REVERT: F 316 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8128 (tp30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1199 time to fit residues: 7.6998 Evaluate side-chains 40 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 30.0000 chunk 116 optimal weight: 0.6980 overall best weight: 4.6986 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.8052 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= 0.204 Angle : 0.810 13.800 20515 Z= 0.403 Chirality : 0.045 0.172 2275 Planarity : 0.006 0.088 2630 Dihedral : 5.548 31.743 2095 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.80 % 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: -2.05 (0.18), residues: 1865 helix: -0.98 (0.19), residues: 670 sheet: 1.12 (0.52), residues: 110 loop : -1.95 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 86 HIS 0.002 0.001 HIS E 73 PHE 0.009 0.001 PHE D 262 TYR 0.028 0.001 TYR H 294 ARG 0.006 0.001 ARG F 210 ********************** 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 47 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 184 ASP cc_start: 0.9037 (p0) cc_final: 0.8407 (t0) REVERT: F 211 ASP cc_start: 0.8541 (p0) cc_final: 0.7465 (t0) REVERT: F 299 MET cc_start: 0.8818 (ppp) cc_final: 0.8577 (ppp) REVERT: F 305 MET cc_start: 0.8297 (mmt) cc_final: 0.8066 (mmt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1236 time to fit residues: 7.4880 Evaluate side-chains 39 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 135 optimal weight: 0.0020 chunk 21 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 0.3980 chunk 61 optimal weight: 0.0070 chunk 150 optimal weight: 0.0770 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 overall best weight: 0.1122 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.078271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070924 restraints weight = 14867.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072347 restraints weight = 9479.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073422 restraints weight = 6529.561| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.8604 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= 0.174 Angle : 0.798 13.044 20515 Z= 0.395 Chirality : 0.045 0.167 2275 Planarity : 0.005 0.044 2630 Dihedral : 5.319 33.822 2095 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.33 % Favored : 87.13 % 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: -2.00 (0.18), residues: 1865 helix: -0.85 (0.20), residues: 650 sheet: -0.13 (0.32), residues: 240 loop : -2.01 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 86 HIS 0.002 0.000 HIS E 88 PHE 0.007 0.001 PHE E 31 TYR 0.014 0.001 TYR H 294 ARG 0.006 0.001 ARG D 147 =============================================================================== Job complete usr+sys time: 1924.05 seconds wall clock time: 36 minutes 0.63 seconds (2160.63 seconds total)