Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 16:13:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/04_2023/7upr_26674_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/04_2023/7upr_26674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/04_2023/7upr_26674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/04_2023/7upr_26674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/04_2023/7upr_26674_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/04_2023/7upr_26674_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.067 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 15 5.49 5 Mg 4 5.21 5 S 79 5.16 5 C 7976 2.51 5 N 2286 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E ARG 199": "NH1" <-> "NH2" Residue "E ASP 205": "OD1" <-> "OD2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E GLU 286": "OE1" <-> "OE2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D ASP 224": "OD1" <-> "OD2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 221": "OD1" <-> "OD2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F ARG 304": "NH1" <-> "NH2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12780 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2350 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 285} Chain breaks: 1 Chain: "B" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2181 Classifications: {'peptide': 277} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 264} Chain breaks: 2 Chain: "E" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2364 Classifications: {'peptide': 300} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 287} Chain breaks: 1 Chain: "D" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2357 Classifications: {'peptide': 299} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 286} Chain breaks: 1 Chain: "F" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2119 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 12, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1200 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 673 Unresolved non-hydrogen angles: 849 Unresolved non-hydrogen dihedrals: 556 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 8, 'GLU:plan': 9, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 323 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.23, per 1000 atoms: 0.57 Number of scatterers: 12780 At special positions: 0 Unit cell: (75.712, 133.12, 137.28, 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 79 16.00 P 15 15.00 Mg 4 11.99 O 2420 8.00 N 2286 7.00 C 7976 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 - 3.50 Amino acid : False - 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: 5.88 Conformation dependent library (CDL) restraints added in 2.2 seconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 7 sheets defined 46.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 71 through 79 removed outlier: 4.599A pdb=" N HIS C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 108 through 111 No H-bonds generated for 'chain 'C' and resid 108 through 111' Processing helix chain 'C' and resid 114 through 117 No H-bonds generated for 'chain 'C' and resid 114 through 117' Processing helix chain 'C' and resid 139 through 148 Processing helix chain 'C' and resid 170 through 183 removed outlier: 3.809A pdb=" N PHE C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 207 through 220 removed outlier: 3.599A pdb=" N MET C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.543A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 246 through 250' Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 284 through 291 Processing helix chain 'C' and resid 298 through 315 Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.002A pdb=" N ASP C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALA C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 62 No H-bonds generated for 'chain 'B' and resid 59 through 62' Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.510A pdb=" N ALA B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 171 through 183 removed outlier: 3.837A pdb=" N PHE B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 247 through 250 No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.598A pdb=" N GLU B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.053A pdb=" N GLU B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR B 314 " --> pdb=" O CYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 removed outlier: 4.037A pdb=" N ASP B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.737A pdb=" N ALA E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU E 56 " --> pdb=" O GLN E 52 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 4.519A pdb=" N HIS E 79 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 98 through 106 Processing helix chain 'E' and resid 108 through 111 No H-bonds generated for 'chain 'E' and resid 108 through 111' Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 170 through 183 removed outlier: 3.743A pdb=" N PHE E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 207 through 220 removed outlier: 3.585A pdb=" N MET E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 250 No H-bonds generated for 'chain 'E' and resid 247 through 250' Processing helix chain 'E' and resid 262 through 274 removed outlier: 3.949A pdb=" N LYS E 274 " --> pdb=" O LYS E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 291 Processing helix chain 'E' and resid 298 through 317 removed outlier: 4.133A pdb=" N SER E 317 " --> pdb=" O GLU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 349 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 71 through 79 removed outlier: 4.711A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 108 through 111 No H-bonds generated for 'chain 'D' and resid 108 through 111' Processing helix chain 'D' and resid 114 through 117 No H-bonds generated for 'chain 'D' and resid 114 through 117' Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.752A pdb=" N PHE D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 207 through 220 removed outlier: 3.598A pdb=" N MET D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 250 No H-bonds generated for 'chain 'D' and resid 247 through 250' Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.961A pdb=" N LYS D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 291 Processing helix chain 'D' and resid 296 through 316 removed outlier: 3.996A pdb=" N LYS D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 349 removed outlier: 3.716A pdb=" N ARG D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 3.679A pdb=" N ALA F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS F 79 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 111 removed outlier: 3.661A pdb=" N ASP F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 139 through 149 removed outlier: 4.037A pdb=" N ALA F 143 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 183 Processing helix chain 'F' and resid 194 through 197 No H-bonds generated for 'chain 'F' and resid 194 through 197' Processing helix chain 'F' and resid 210 through 220 removed outlier: 3.699A pdb=" N MET F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 296 through 312 removed outlier: 3.823A pdb=" N ARG F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 333 through 346 Processing helix chain 'A' and resid 97 through 109 removed outlier: 4.221A pdb=" N ILE A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.839A pdb=" N ALA A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 183 Processing helix chain 'A' and resid 209 through 226 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.766A pdb=" N GLU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 315 removed outlier: 4.086A pdb=" N LYS A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 Processing sheet with id= A, first strand: chain 'C' and resid 253 through 256 removed outlier: 6.050A pdb=" N SER C 187 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N MET C 234 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE C 189 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA C 236 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 191 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ARG C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N PHE C 190 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 253 through 257 removed outlier: 4.119A pdb=" N ALA B 236 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ARG B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE B 190 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 253 through 257 removed outlier: 6.062A pdb=" N SER E 187 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N MET E 234 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE E 189 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA E 236 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE E 191 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE E 190 " --> pdb=" O ARG E 153 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP E 192 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 253 through 256 removed outlier: 6.114A pdb=" N SER D 187 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N MET D 234 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE D 189 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA D 236 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ARG D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE D 190 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 254 through 256 removed outlier: 6.001A pdb=" N LEU F 130 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU F 131 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY F 235 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE F 189 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA F 236 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE F 191 " --> pdb=" O ALA F 236 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 129 through 133 removed outlier: 6.507A pdb=" N THR A 253 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR A 132 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE A 255 " --> pdb=" O TYR A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 153 through 156 452 hydrogen bonds defined for protein. 1341 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: 3.41 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4305 1.35 - 1.46: 2526 1.46 - 1.58: 5976 1.58 - 1.70: 25 1.70 - 1.81: 133 Bond restraints: 12965 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.17e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.11e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.09e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.98e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.83e+01 ... (remaining 12960 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.44: 505 107.44 - 114.56: 7936 114.56 - 121.68: 6195 121.68 - 128.81: 2830 128.81 - 135.93: 84 Bond angle restraints: 17550 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 119.95 19.92 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 ... (remaining 17545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7127 17.80 - 35.60: 625 35.60 - 53.41: 161 53.41 - 71.21: 34 71.21 - 89.01: 20 Dihedral angle restraints: 7967 sinusoidal: 3037 harmonic: 4930 Sorted by residual: dihedral pdb=" CA GLU D 50 " pdb=" C GLU D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA CYS B 137 " pdb=" C CYS B 137 " pdb=" N GLY B 138 " pdb=" CA GLY B 138 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA GLN F 158 " pdb=" C GLN F 158 " pdb=" N PRO F 159 " pdb=" CA PRO F 159 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1376 0.031 - 0.062: 439 0.062 - 0.093: 134 0.093 - 0.125: 90 0.125 - 0.156: 6 Chirality restraints: 2045 Sorted by residual: chirality pdb=" CA PRO F 186 " pdb=" N PRO F 186 " pdb=" C PRO F 186 " pdb=" CB PRO F 186 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" C1' ATP B 501 " pdb=" C2' ATP B 501 " pdb=" N9 ATP B 501 " pdb=" O4' ATP B 501 " both_signs ideal model delta sigma weight residual False 2.41 2.56 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" C1' ATP F 501 " pdb=" C2' ATP F 501 " pdb=" N9 ATP F 501 " pdb=" O4' ATP F 501 " both_signs ideal model delta sigma weight residual False 2.41 2.55 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2042 not shown) Planarity restraints: 2241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 158 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO F 159 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 159 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 159 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 109 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO B 110 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 259 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO F 260 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 260 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 260 " 0.015 5.00e-02 4.00e+02 ... (remaining 2238 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 179 2.63 - 3.20: 11351 3.20 - 3.76: 20062 3.76 - 4.33: 25542 4.33 - 4.90: 42448 Nonbonded interactions: 99582 Sorted by model distance: nonbonded pdb=" O2B ATP B 501 " pdb="MG MG B 502 " model vdw 2.062 2.170 nonbonded pdb=" O2B ATP E 501 " pdb="MG MG E 502 " model vdw 2.067 2.170 nonbonded pdb=" O2B ATP D 501 " pdb="MG MG D 502 " model vdw 2.069 2.170 nonbonded pdb=" O2B ATP C 501 " pdb="MG MG C 502 " model vdw 2.093 2.170 nonbonded pdb=" O3G ATP B 501 " pdb="MG MG B 502 " model vdw 2.132 2.170 ... (remaining 99577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'F' and ((resid 86 through 94 and (name N or name CA or name C or name O \ or name CB )) or resid 95 or (resid 96 through 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 or (resid 129 through 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 or (resid 134 through 1 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 136 or (res \ id 137 and (name N or name CA or name C or name O or name CB )) or resid 138 or \ (resid 139 through 150 and (name N or name CA or name C or name O or name CB )) \ or resid 151 or (resid 152 through 161 and (name N or name CA or name C or name \ O or name CB )) or (resid 169 through 197 and (name N or name CA or name C or na \ me O or name CB )) or (resid 208 through 221 and (name N or name CA or name C or \ name O or name CB )) or resid 222 or (resid 223 through 234 and (name N or name \ CA or name C or name O or name CB )) or (resid 235 through 258 and (name N or n \ ame CA or name C or name O or name CB )) or resid 259 or (resid 260 through 292 \ and (name N or name CA or name C or name O or name CB )) or resid 293 or (resid \ 294 through 295 and (name N or name CA or name C or name O or name CB )) or resi \ d 296 or (resid 297 through 298 and (name N or name CA or name C or name O or na \ me CB )) or resid 299 through 301 or (resid 302 through 303 and (name N or name \ CA or name C or name O or name CB )) or resid 304 or (resid 305 through 307 and \ (name N or name CA or name C or name O or name CB )) or resid 308 through 309 or \ (resid 310 through 311 and (name N or name CA or name C or name O or name CB )) \ or resid 312 or (resid 313 through 314 and (name N or name CA or name C or name \ O or name CB )) or resid 315 or (resid 316 through 347 and (name N or name CA o \ r name C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 55 through 199 or resid 210 through 351 or resid 501 throu \ gh 502)) selection = (chain 'D' and (resid 55 through 199 or resid 210 through 351 or resid 501 throu \ gh 502)) selection = (chain 'E' and (resid 55 through 199 or resid 210 through 317 or resid 328 throu \ gh 351 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 8.120 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.780 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.004 0.085 12965 Z= 0.272 Angle : 0.796 19.923 17550 Z= 0.616 Chirality : 0.039 0.156 2045 Planarity : 0.003 0.048 2241 Dihedral : 15.491 89.009 4729 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -3.02 (0.18), residues: 1648 helix: -1.14 (0.16), residues: 771 sheet: -2.78 (0.37), residues: 132 loop : -2.79 (0.19), residues: 745 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 283 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 35 residues processed: 330 average time/residue: 0.2632 time to fit residues: 123.2389 Evaluate side-chains 219 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1181 time to fit residues: 9.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS E 47 GLN E 52 GLN E 79 HIS E 119 ASN E 193 GLN E 264 GLN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 12965 Z= 0.322 Angle : 0.624 10.215 17550 Z= 0.305 Chirality : 0.043 0.174 2045 Planarity : 0.004 0.045 2241 Dihedral : 4.832 66.301 1781 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1648 helix: -0.07 (0.18), residues: 797 sheet: -2.40 (0.36), residues: 148 loop : -2.16 (0.22), residues: 703 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 230 average time/residue: 0.2669 time to fit residues: 88.1248 Evaluate side-chains 195 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1468 time to fit residues: 6.8742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 0.0470 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS E 119 ASN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12965 Z= 0.175 Angle : 0.547 11.044 17550 Z= 0.267 Chirality : 0.040 0.153 2045 Planarity : 0.003 0.043 2241 Dihedral : 4.844 62.435 1781 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -1.11 (0.21), residues: 1648 helix: 0.47 (0.19), residues: 796 sheet: -1.91 (0.36), residues: 161 loop : -1.87 (0.23), residues: 691 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 219 average time/residue: 0.2369 time to fit residues: 76.0931 Evaluate side-chains 193 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1120 time to fit residues: 4.5147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 50.0000 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 40.0000 chunk 159 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN C 193 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS E 79 HIS E 119 ASN E 264 GLN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 12965 Z= 0.372 Angle : 0.647 9.442 17550 Z= 0.321 Chirality : 0.044 0.153 2045 Planarity : 0.004 0.047 2241 Dihedral : 5.478 59.578 1781 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer Outliers : 3.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.90 (0.21), residues: 1648 helix: 0.58 (0.19), residues: 789 sheet: -1.56 (0.43), residues: 140 loop : -1.73 (0.23), residues: 719 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 28 residues processed: 217 average time/residue: 0.2701 time to fit residues: 84.2703 Evaluate side-chains 200 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1754 time to fit residues: 10.0966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 136 optimal weight: 0.0370 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 238 ASN B 281 HIS E 119 ASN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 12965 Z= 0.180 Angle : 0.568 11.428 17550 Z= 0.276 Chirality : 0.041 0.168 2045 Planarity : 0.003 0.042 2241 Dihedral : 5.252 59.214 1781 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.55 (0.22), residues: 1648 helix: 0.84 (0.20), residues: 789 sheet: -1.42 (0.41), residues: 154 loop : -1.50 (0.24), residues: 705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 205 average time/residue: 0.2552 time to fit residues: 75.6262 Evaluate side-chains 176 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1102 time to fit residues: 4.1079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN B 281 HIS E 119 ASN E 337 HIS D 79 HIS F 124 GLN F 230 GLN F 238 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12965 Z= 0.203 Angle : 0.566 10.777 17550 Z= 0.275 Chirality : 0.041 0.150 2045 Planarity : 0.003 0.056 2241 Dihedral : 5.199 57.888 1781 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.36 (0.22), residues: 1648 helix: 0.96 (0.20), residues: 795 sheet: -1.30 (0.41), residues: 159 loop : -1.38 (0.24), residues: 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 196 average time/residue: 0.2591 time to fit residues: 74.1162 Evaluate side-chains 177 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1285 time to fit residues: 5.4669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 116 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 206 HIS ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS F 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 12965 Z= 0.168 Angle : 0.563 11.524 17550 Z= 0.273 Chirality : 0.040 0.149 2045 Planarity : 0.003 0.041 2241 Dihedral : 5.097 56.771 1781 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.21 (0.22), residues: 1648 helix: 1.12 (0.20), residues: 788 sheet: -1.17 (0.41), residues: 159 loop : -1.34 (0.24), residues: 701 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 191 average time/residue: 0.2440 time to fit residues: 68.9209 Evaluate side-chains 172 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1156 time to fit residues: 3.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 144 optimal weight: 40.0000 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 54 GLN E 119 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS F 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 12965 Z= 0.229 Angle : 0.591 10.875 17550 Z= 0.286 Chirality : 0.041 0.154 2045 Planarity : 0.003 0.049 2241 Dihedral : 5.169 57.140 1781 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.19 (0.22), residues: 1648 helix: 1.08 (0.20), residues: 801 sheet: -1.00 (0.42), residues: 159 loop : -1.36 (0.24), residues: 688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 182 average time/residue: 0.2524 time to fit residues: 68.2251 Evaluate side-chains 174 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1260 time to fit residues: 4.7382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 50.0000 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.2980 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS F 79 HIS F 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 12965 Z= 0.253 Angle : 0.617 11.458 17550 Z= 0.300 Chirality : 0.042 0.159 2045 Planarity : 0.003 0.042 2241 Dihedral : 5.324 58.863 1781 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.19 (0.22), residues: 1648 helix: 1.06 (0.20), residues: 799 sheet: -1.00 (0.42), residues: 160 loop : -1.31 (0.24), residues: 689 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 179 average time/residue: 0.2827 time to fit residues: 72.9402 Evaluate side-chains 171 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.631 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3089 time to fit residues: 3.4110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 151 optimal weight: 30.0000 chunk 130 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN E 119 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS F 79 HIS F 124 GLN F 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12965 Z= 0.190 Angle : 0.595 11.267 17550 Z= 0.287 Chirality : 0.041 0.151 2045 Planarity : 0.003 0.056 2241 Dihedral : 5.221 58.188 1781 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: -0.05 (0.22), residues: 1648 helix: 1.18 (0.20), residues: 797 sheet: -0.88 (0.42), residues: 159 loop : -1.26 (0.24), residues: 692 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.2730 time to fit residues: 69.0969 Evaluate side-chains 167 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1184 time to fit residues: 2.4490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 0.0040 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 131 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN D 79 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092796 restraints weight = 21367.172| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.49 r_work: 0.3147 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12965 Z= 0.170 Angle : 0.610 11.602 17550 Z= 0.296 Chirality : 0.040 0.188 2045 Planarity : 0.003 0.049 2241 Dihedral : 5.171 57.113 1781 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.01 (0.22), residues: 1648 helix: 1.24 (0.20), residues: 796 sheet: -0.93 (0.42), residues: 164 loop : -1.21 (0.25), residues: 688 =============================================================================== Job complete usr+sys time: 2751.15 seconds wall clock time: 50 minutes 32.83 seconds (3032.83 seconds total)