Starting phenix.real_space_refine on Thu Feb 15 16:31:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/02_2024/7upr_26674_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/02_2024/7upr_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_26674/02_2024/7upr_26674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/02_2024/7upr_26674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/02_2024/7upr_26674_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upr_26674/02_2024/7upr_26674_updated.pdb" } resolution = 3.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.24, 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: 5.55 Conformation dependent library (CDL) restraints added in 2.4 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: 2.70 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: 3.67 Time building geometry restraints manager: 5.56 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: 7210 17.80 - 35.60: 678 35.60 - 53.41: 180 53.41 - 71.21: 34 71.21 - 89.01: 20 Dihedral angle restraints: 8122 sinusoidal: 3192 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 8119 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: 1.770 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: 7.440 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 37.420 Find NCS groups from input model: 1.050 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.900 ------------------------------------------------------------------------------- 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 : 15.822 89.009 4884 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 % Allowed : 14.81 % Favored : 81.01 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 90 HIS 0.003 0.000 HIS B 227 PHE 0.005 0.001 PHE B 216 TYR 0.004 0.000 TYR D 132 ARG 0.001 0.000 ARG C 153 *********************** 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 : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6893 (pp) REVERT: C 279 ASP cc_start: 0.8334 (t70) cc_final: 0.8006 (t70) REVERT: B 68 LYS cc_start: 0.8695 (mppt) cc_final: 0.8461 (mppt) REVERT: B 74 MET cc_start: 0.8259 (mtt) cc_final: 0.7947 (mtt) REVERT: B 184 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8005 (pp) REVERT: B 341 GLU cc_start: 0.8286 (tp30) cc_final: 0.7941 (mm-30) REVERT: E 45 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6130 (ttm-80) REVERT: E 60 LYS cc_start: 0.9128 (tptm) cc_final: 0.8927 (ttpt) REVERT: D 305 ASP cc_start: 0.8209 (t0) cc_final: 0.7754 (t0) REVERT: F 98 ASP cc_start: 0.7944 (t0) cc_final: 0.7559 (t0) REVERT: F 102 ASP cc_start: 0.7456 (m-30) cc_final: 0.7183 (m-30) REVERT: F 131 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7053 (mp) REVERT: F 199 ARG cc_start: 0.7762 (ttp-110) cc_final: 0.7559 (ttm110) REVERT: F 290 GLU cc_start: 0.7947 (mp0) cc_final: 0.7665 (mp0) REVERT: F 345 LYS cc_start: 0.8395 (mmtm) cc_final: 0.8174 (pptt) REVERT: A 309 LEU cc_start: 0.8131 (mp) cc_final: 0.7865 (mp) outliers start: 53 outliers final: 35 residues processed: 330 average time/residue: 0.2702 time to fit residues: 127.0877 Evaluate side-chains 232 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 278 VAL 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: 5.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 0.0970 chunk 50 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 66 ASN ** 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 52 GLN E 119 ASN E 193 GLN E 264 GLN E 332 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1398 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= 0.216 Angle : 0.556 10.378 17550 Z= 0.272 Chirality : 0.041 0.150 2045 Planarity : 0.003 0.044 2241 Dihedral : 10.351 79.839 2010 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.65 % Allowed : 19.54 % Favored : 75.81 % 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: -1.70 (0.20), residues: 1648 helix: 0.03 (0.19), residues: 797 sheet: -2.43 (0.36), residues: 148 loop : -2.18 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 220 HIS 0.006 0.001 HIS B 281 PHE 0.014 0.001 PHE B 351 TYR 0.028 0.001 TYR B 132 ARG 0.004 0.000 ARG D 280 *********************** 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 267 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 208 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6990 (pp) REVERT: C 121 ARG cc_start: 0.8361 (tpt90) cc_final: 0.8104 (tpp80) REVERT: C 279 ASP cc_start: 0.8131 (t70) cc_final: 0.7750 (t70) REVERT: C 280 ARG cc_start: 0.8826 (tmm-80) cc_final: 0.8579 (tmm-80) REVERT: B 74 MET cc_start: 0.8254 (mtt) cc_final: 0.7935 (mtt) REVERT: B 130 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8431 (tt) REVERT: B 184 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8004 (pp) REVERT: B 341 GLU cc_start: 0.8296 (tp30) cc_final: 0.8088 (tp30) REVERT: E 45 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5920 (ttm-80) REVERT: E 74 MET cc_start: 0.7987 (tpp) cc_final: 0.7432 (mpp) REVERT: E 292 ASP cc_start: 0.7782 (t70) cc_final: 0.7558 (t0) REVERT: E 332 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.7054 (pp30) REVERT: D 290 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7867 (mm-30) REVERT: D 305 ASP cc_start: 0.8354 (t0) cc_final: 0.7829 (t0) REVERT: F 98 ASP cc_start: 0.7727 (t0) cc_final: 0.7303 (t0) REVERT: F 102 ASP cc_start: 0.7458 (m-30) cc_final: 0.6954 (m-30) REVERT: F 199 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7368 (ttm110) REVERT: F 345 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8093 (pptt) outliers start: 59 outliers final: 41 residues processed: 258 average time/residue: 0.2512 time to fit residues: 92.1416 Evaluate side-chains 232 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 162 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 148 optimal weight: 30.0000 chunk 51 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 B 259 GLN B 281 HIS E 47 GLN E 79 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12965 Z= 0.248 Angle : 0.559 11.048 17550 Z= 0.277 Chirality : 0.041 0.150 2045 Planarity : 0.003 0.045 2241 Dihedral : 10.353 80.714 2001 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 5.12 % Allowed : 21.43 % Favored : 73.44 % 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: -1.10 (0.21), residues: 1648 helix: 0.49 (0.19), residues: 798 sheet: -1.95 (0.40), residues: 135 loop : -1.90 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 220 HIS 0.008 0.001 HIS B 281 PHE 0.009 0.001 PHE B 154 TYR 0.008 0.001 TYR E 132 ARG 0.007 0.000 ARG D 45 *********************** 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 263 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 198 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8375 (tpt90) cc_final: 0.8146 (tpp80) REVERT: C 279 ASP cc_start: 0.8170 (t70) cc_final: 0.7874 (t70) REVERT: C 280 ARG cc_start: 0.8785 (tmm-80) cc_final: 0.8567 (tmm-80) REVERT: B 68 LYS cc_start: 0.8861 (mptt) cc_final: 0.8660 (mppt) REVERT: B 74 MET cc_start: 0.8278 (mtt) cc_final: 0.7946 (mtt) REVERT: B 184 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8042 (pp) REVERT: B 341 GLU cc_start: 0.8313 (tp30) cc_final: 0.8104 (tp30) REVERT: E 45 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.5940 (ttm-80) REVERT: E 74 MET cc_start: 0.8057 (tpp) cc_final: 0.7512 (mpp) REVERT: E 292 ASP cc_start: 0.7864 (t70) cc_final: 0.7607 (t0) REVERT: D 290 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7908 (mm-30) REVERT: D 305 ASP cc_start: 0.8389 (t0) cc_final: 0.7812 (t0) REVERT: F 98 ASP cc_start: 0.7725 (t0) cc_final: 0.7224 (t0) REVERT: F 102 ASP cc_start: 0.7496 (m-30) cc_final: 0.6941 (m-30) REVERT: F 169 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: F 199 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7424 (ttm110) REVERT: F 211 MET cc_start: 0.7587 (tmm) cc_final: 0.7377 (tmm) REVERT: F 275 ASN cc_start: 0.7704 (p0) cc_final: 0.7468 (p0) REVERT: F 345 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8199 (pptt) REVERT: A 309 LEU cc_start: 0.8374 (mp) cc_final: 0.8172 (mp) outliers start: 65 outliers final: 45 residues processed: 252 average time/residue: 0.2517 time to fit residues: 91.0334 Evaluate side-chains 232 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 285 LEU 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: 4.9990 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 30.0000 chunk 159 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 61 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** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12965 Z= 0.259 Angle : 0.553 10.146 17550 Z= 0.274 Chirality : 0.041 0.157 2045 Planarity : 0.003 0.043 2241 Dihedral : 10.361 81.228 1992 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.36 % Allowed : 22.22 % Favored : 72.42 % 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: -0.81 (0.21), residues: 1648 helix: 0.67 (0.19), residues: 801 sheet: -1.82 (0.40), residues: 145 loop : -1.68 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.003 0.001 HIS D 79 PHE 0.012 0.001 PHE E 117 TYR 0.020 0.001 TYR B 132 ARG 0.003 0.000 ARG A 304 *********************** 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 260 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 192 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8380 (tpt90) cc_final: 0.8159 (tpp80) REVERT: C 279 ASP cc_start: 0.8030 (t70) cc_final: 0.7737 (t70) REVERT: C 280 ARG cc_start: 0.8883 (tmm-80) cc_final: 0.8429 (tmm-80) REVERT: C 281 HIS cc_start: 0.7752 (p-80) cc_final: 0.7109 (p-80) REVERT: B 74 MET cc_start: 0.8328 (mtt) cc_final: 0.7969 (mtt) REVERT: B 184 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8015 (pp) REVERT: B 341 GLU cc_start: 0.8337 (tp30) cc_final: 0.8108 (tp30) REVERT: E 45 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6012 (ttm-80) REVERT: E 74 MET cc_start: 0.8042 (tpp) cc_final: 0.7543 (mpp) REVERT: E 199 ARG cc_start: 0.8437 (ttm110) cc_final: 0.8187 (ttm110) REVERT: E 292 ASP cc_start: 0.7912 (t70) cc_final: 0.7651 (t0) REVERT: D 290 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7954 (mm-30) REVERT: F 79 HIS cc_start: 0.7547 (m-70) cc_final: 0.7323 (m170) REVERT: F 96 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7163 (pp) REVERT: F 102 ASP cc_start: 0.7442 (m-30) cc_final: 0.6805 (m-30) REVERT: F 169 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: F 199 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7451 (ttm110) REVERT: F 207 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6147 (pp20) REVERT: F 211 MET cc_start: 0.7707 (tmm) cc_final: 0.7477 (tmm) REVERT: F 275 ASN cc_start: 0.7667 (p0) cc_final: 0.7407 (p0) REVERT: F 345 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8071 (pptt) outliers start: 68 outliers final: 51 residues processed: 246 average time/residue: 0.2569 time to fit residues: 90.5054 Evaluate side-chains 231 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.0470 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 0.0970 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 281 HIS E 119 ASN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12965 Z= 0.170 Angle : 0.525 11.384 17550 Z= 0.260 Chirality : 0.040 0.146 2045 Planarity : 0.003 0.043 2241 Dihedral : 10.141 81.373 1992 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 5.20 % Allowed : 23.17 % Favored : 71.63 % 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: -0.52 (0.21), residues: 1648 helix: 0.88 (0.20), residues: 803 sheet: -1.49 (0.41), residues: 140 loop : -1.54 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.006 0.000 HIS B 281 PHE 0.010 0.001 PHE B 154 TYR 0.028 0.001 TYR B 132 ARG 0.003 0.000 ARG D 280 *********************** 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 262 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 196 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 121 ARG cc_start: 0.8358 (tpt90) cc_final: 0.8144 (tpp80) REVERT: C 169 GLU cc_start: 0.8515 (tp30) cc_final: 0.8282 (tp30) REVERT: C 251 MET cc_start: 0.8815 (mtt) cc_final: 0.8594 (mtt) REVERT: C 279 ASP cc_start: 0.7991 (t70) cc_final: 0.7788 (t70) REVERT: B 74 MET cc_start: 0.8336 (mtt) cc_final: 0.7967 (mtt) REVERT: B 184 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8015 (pp) REVERT: B 341 GLU cc_start: 0.8299 (tp30) cc_final: 0.8083 (tp30) REVERT: E 45 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5949 (ttm-80) REVERT: E 74 MET cc_start: 0.8012 (tpp) cc_final: 0.7555 (mpp) REVERT: E 121 ARG cc_start: 0.8330 (tpp80) cc_final: 0.7676 (tpp80) REVERT: E 199 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8156 (ttm110) REVERT: E 292 ASP cc_start: 0.7852 (t70) cc_final: 0.7560 (t0) REVERT: D 290 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7941 (mm-30) REVERT: D 305 ASP cc_start: 0.8373 (t0) cc_final: 0.7802 (t0) REVERT: F 96 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7209 (pp) REVERT: F 98 ASP cc_start: 0.7703 (t0) cc_final: 0.7208 (t0) REVERT: F 102 ASP cc_start: 0.7402 (m-30) cc_final: 0.6792 (m-30) REVERT: F 169 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: F 199 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7432 (ttm110) REVERT: F 207 GLU cc_start: 0.6460 (mm-30) cc_final: 0.6055 (pp20) REVERT: F 275 ASN cc_start: 0.7652 (p0) cc_final: 0.7344 (p0) REVERT: F 345 LYS cc_start: 0.8402 (mmtm) cc_final: 0.8141 (pptt) outliers start: 66 outliers final: 51 residues processed: 247 average time/residue: 0.2464 time to fit residues: 87.9061 Evaluate side-chains 234 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 179 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 159 optimal weight: 9.9990 chunk 132 optimal weight: 0.0050 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2468 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= 0.178 Angle : 0.537 10.933 17550 Z= 0.263 Chirality : 0.040 0.148 2045 Planarity : 0.003 0.040 2241 Dihedral : 9.929 81.344 1989 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.12 % Allowed : 23.48 % Favored : 71.39 % 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: -0.34 (0.22), residues: 1648 helix: 1.03 (0.20), residues: 801 sheet: -1.40 (0.41), residues: 146 loop : -1.43 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.007 0.001 HIS B 281 PHE 0.013 0.001 PHE E 117 TYR 0.005 0.001 TYR F 132 ARG 0.003 0.000 ARG E 199 *********************** 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 250 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 185 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8565 (tm-30) REVERT: C 121 ARG cc_start: 0.8351 (tpt90) cc_final: 0.8133 (tpp80) REVERT: C 169 GLU cc_start: 0.8518 (tp30) cc_final: 0.8288 (tp30) REVERT: C 279 ASP cc_start: 0.8180 (t70) cc_final: 0.7905 (t70) REVERT: B 74 MET cc_start: 0.8346 (mtt) cc_final: 0.7954 (mtt) REVERT: B 195 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: B 341 GLU cc_start: 0.8315 (tp30) cc_final: 0.8086 (tp30) REVERT: E 74 MET cc_start: 0.8023 (tpp) cc_final: 0.7563 (mpp) REVERT: E 121 ARG cc_start: 0.7961 (tpp80) cc_final: 0.7738 (tpp80) REVERT: E 292 ASP cc_start: 0.7827 (t70) cc_final: 0.7586 (t0) REVERT: E 312 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: D 290 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7929 (mm-30) REVERT: D 305 ASP cc_start: 0.8369 (t0) cc_final: 0.7821 (t0) REVERT: F 96 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7218 (pp) REVERT: F 98 ASP cc_start: 0.7696 (t0) cc_final: 0.7155 (t0) REVERT: F 102 ASP cc_start: 0.7412 (m-30) cc_final: 0.6769 (m-30) REVERT: F 158 GLN cc_start: 0.5974 (tp40) cc_final: 0.5709 (mm-40) REVERT: F 169 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: F 199 ARG cc_start: 0.7816 (ttp-110) cc_final: 0.7443 (ttm110) REVERT: F 207 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6137 (pp20) REVERT: F 275 ASN cc_start: 0.7622 (p0) cc_final: 0.7335 (p0) REVERT: F 345 LYS cc_start: 0.8389 (mmtm) cc_final: 0.8112 (pptt) outliers start: 65 outliers final: 50 residues processed: 236 average time/residue: 0.2394 time to fit residues: 82.3948 Evaluate side-chains 235 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 116 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2542 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= 0.179 Angle : 0.540 11.417 17550 Z= 0.264 Chirality : 0.040 0.154 2045 Planarity : 0.003 0.041 2241 Dihedral : 9.822 81.788 1983 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.44 % Allowed : 23.72 % Favored : 70.84 % 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: -0.23 (0.22), residues: 1648 helix: 1.14 (0.20), residues: 789 sheet: -1.22 (0.42), residues: 146 loop : -1.40 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.007 0.001 HIS F 79 PHE 0.009 0.001 PHE D 351 TYR 0.005 0.001 TYR F 132 ARG 0.010 0.000 ARG D 280 *********************** 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 259 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 190 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8584 (tm-30) REVERT: C 112 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8321 (ptpp) REVERT: C 121 ARG cc_start: 0.8338 (tpt90) cc_final: 0.8117 (tpp80) REVERT: C 169 GLU cc_start: 0.8513 (tp30) cc_final: 0.8279 (tp30) REVERT: C 251 MET cc_start: 0.8768 (mtt) cc_final: 0.8538 (mtt) REVERT: C 266 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: C 279 ASP cc_start: 0.8169 (t70) cc_final: 0.7876 (t70) REVERT: B 74 MET cc_start: 0.8350 (mtt) cc_final: 0.7952 (mtt) REVERT: B 195 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: B 341 GLU cc_start: 0.8316 (tp30) cc_final: 0.8086 (tp30) REVERT: E 74 MET cc_start: 0.8026 (tpp) cc_final: 0.7562 (mpp) REVERT: E 121 ARG cc_start: 0.7971 (tpp80) cc_final: 0.7738 (tpp80) REVERT: E 187 SER cc_start: 0.9416 (p) cc_final: 0.9029 (m) REVERT: E 292 ASP cc_start: 0.7807 (t70) cc_final: 0.7533 (t0) REVERT: E 312 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7567 (ttm170) REVERT: D 305 ASP cc_start: 0.8372 (t0) cc_final: 0.7798 (t0) REVERT: F 96 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7232 (pp) REVERT: F 98 ASP cc_start: 0.7701 (t0) cc_final: 0.7125 (t0) REVERT: F 102 ASP cc_start: 0.7440 (m-30) cc_final: 0.6757 (m-30) REVERT: F 116 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8307 (tt) REVERT: F 169 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: F 199 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7475 (ttm110) REVERT: F 275 ASN cc_start: 0.7606 (p0) cc_final: 0.7311 (p0) REVERT: F 345 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8108 (pptt) outliers start: 69 outliers final: 55 residues processed: 241 average time/residue: 0.2331 time to fit residues: 82.1491 Evaluate side-chains 242 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 179 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.0060 chunk 47 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 144 optimal weight: 0.0870 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 119 ASN E 206 HIS ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN E 337 HIS D 79 HIS F 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 12965 Z= 0.147 Angle : 0.547 11.399 17550 Z= 0.265 Chirality : 0.040 0.154 2045 Planarity : 0.003 0.041 2241 Dihedral : 9.598 81.843 1983 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.81 % Allowed : 24.67 % Favored : 70.53 % 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: -0.17 (0.22), residues: 1648 helix: 1.17 (0.20), residues: 796 sheet: -1.08 (0.42), residues: 146 loop : -1.40 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.005 0.000 HIS F 79 PHE 0.018 0.001 PHE C 117 TYR 0.004 0.001 TYR C 167 ARG 0.008 0.000 ARG D 280 *********************** 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 244 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8300 (ptpp) REVERT: C 121 ARG cc_start: 0.8339 (tpt90) cc_final: 0.8115 (tpp80) REVERT: C 169 GLU cc_start: 0.8468 (tp30) cc_final: 0.8136 (tp30) REVERT: C 251 MET cc_start: 0.8774 (mtt) cc_final: 0.8557 (mtt) REVERT: C 266 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: C 279 ASP cc_start: 0.8229 (t70) cc_final: 0.7940 (t70) REVERT: B 74 MET cc_start: 0.8339 (mtt) cc_final: 0.7921 (mtt) REVERT: B 195 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: B 341 GLU cc_start: 0.8302 (tp30) cc_final: 0.7959 (mm-30) REVERT: E 74 MET cc_start: 0.8003 (tpp) cc_final: 0.7589 (mpp) REVERT: E 121 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7761 (tpp80) REVERT: E 187 SER cc_start: 0.9382 (p) cc_final: 0.9014 (m) REVERT: E 292 ASP cc_start: 0.7771 (t70) cc_final: 0.7491 (t0) REVERT: E 312 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7540 (ttm170) REVERT: D 248 MET cc_start: 0.8512 (tpt) cc_final: 0.8254 (mmm) REVERT: D 305 ASP cc_start: 0.8345 (t0) cc_final: 0.7802 (t0) REVERT: F 96 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7222 (pp) REVERT: F 98 ASP cc_start: 0.7684 (t0) cc_final: 0.7105 (t0) REVERT: F 102 ASP cc_start: 0.7439 (m-30) cc_final: 0.6750 (m-30) REVERT: F 158 GLN cc_start: 0.6306 (mm-40) cc_final: 0.5994 (mm-40) REVERT: F 169 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: F 199 ARG cc_start: 0.7830 (ttp-110) cc_final: 0.7459 (ttm110) REVERT: F 275 ASN cc_start: 0.7561 (p0) cc_final: 0.7296 (p0) REVERT: F 345 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8088 (pptt) outliers start: 61 outliers final: 51 residues processed: 231 average time/residue: 0.2629 time to fit residues: 88.8815 Evaluate side-chains 236 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 179 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 50.0000 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 50.0000 chunk 97 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS C 119 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 119 ASN E 337 HIS D 79 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS F 185 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12965 Z= 0.333 Angle : 0.624 10.621 17550 Z= 0.308 Chirality : 0.043 0.148 2045 Planarity : 0.004 0.044 2241 Dihedral : 10.290 84.099 1983 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.44 % Allowed : 24.43 % Favored : 70.13 % 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: -0.25 (0.22), residues: 1648 helix: 1.02 (0.20), residues: 795 sheet: -0.91 (0.43), residues: 141 loop : -1.37 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 220 HIS 0.012 0.001 HIS F 79 PHE 0.016 0.002 PHE E 154 TYR 0.009 0.001 TYR E 132 ARG 0.009 0.001 ARG D 280 *********************** 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 250 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 181 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8591 (tm-30) REVERT: C 112 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8412 (ptpp) REVERT: C 266 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: C 279 ASP cc_start: 0.8240 (t70) cc_final: 0.7972 (t70) REVERT: B 74 MET cc_start: 0.8412 (mtt) cc_final: 0.7973 (mtt) REVERT: B 341 GLU cc_start: 0.8362 (tp30) cc_final: 0.8127 (tp30) REVERT: E 74 MET cc_start: 0.8067 (tpp) cc_final: 0.7518 (mpp) REVERT: E 121 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7894 (tpp80) REVERT: E 292 ASP cc_start: 0.7898 (t70) cc_final: 0.7571 (t0) REVERT: D 121 ARG cc_start: 0.8949 (tpt-90) cc_final: 0.8723 (tpp80) REVERT: F 96 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7358 (pp) REVERT: F 102 ASP cc_start: 0.7411 (m-30) cc_final: 0.6739 (m-30) REVERT: F 116 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8315 (tt) REVERT: F 158 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6443 (mm-40) REVERT: F 199 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7472 (ttm110) REVERT: F 345 LYS cc_start: 0.8385 (mmtm) cc_final: 0.7964 (pptt) outliers start: 69 outliers final: 52 residues processed: 231 average time/residue: 0.2916 time to fit residues: 96.2132 Evaluate side-chains 231 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 174 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 238 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.0980 chunk 95 optimal weight: 0.4980 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 151 optimal weight: 40.0000 chunk 130 optimal weight: 0.0070 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 E 119 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS D 79 HIS F 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12965 Z= 0.163 Angle : 0.584 11.645 17550 Z= 0.286 Chirality : 0.041 0.216 2045 Planarity : 0.003 0.040 2241 Dihedral : 9.926 84.150 1982 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.57 % Allowed : 25.61 % Favored : 69.82 % 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: -0.09 (0.22), residues: 1648 helix: 1.18 (0.20), residues: 798 sheet: -0.96 (0.42), residues: 146 loop : -1.30 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 90 HIS 0.005 0.001 HIS C 281 PHE 0.013 0.001 PHE B 351 TYR 0.031 0.001 TYR B 132 ARG 0.007 0.000 ARG D 280 ********************** 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 236 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 178 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8339 (ptpp) REVERT: C 224 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7679 (t0) REVERT: C 251 MET cc_start: 0.8747 (mtt) cc_final: 0.8455 (mtt) REVERT: C 279 ASP cc_start: 0.8267 (t70) cc_final: 0.7919 (t70) REVERT: B 74 MET cc_start: 0.8416 (mtt) cc_final: 0.7985 (mtt) REVERT: B 341 GLU cc_start: 0.8310 (tp30) cc_final: 0.8076 (tp30) REVERT: E 74 MET cc_start: 0.8002 (tpp) cc_final: 0.7558 (mpp) REVERT: E 121 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7843 (tpp80) REVERT: E 292 ASP cc_start: 0.7812 (t70) cc_final: 0.7491 (t0) REVERT: E 337 HIS cc_start: 0.7353 (m90) cc_final: 0.7062 (m-70) REVERT: D 86 MET cc_start: 0.8168 (mmm) cc_final: 0.7168 (mmm) REVERT: D 121 ARG cc_start: 0.8933 (tpt-90) cc_final: 0.8703 (tpp80) REVERT: F 96 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7243 (pp) REVERT: F 98 ASP cc_start: 0.7712 (t0) cc_final: 0.7193 (t0) REVERT: F 102 ASP cc_start: 0.7383 (m-30) cc_final: 0.6732 (m-30) REVERT: F 116 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8289 (tt) REVERT: F 158 GLN cc_start: 0.6874 (mm-40) cc_final: 0.6565 (mm-40) REVERT: F 199 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7471 (ttm110) REVERT: F 275 ASN cc_start: 0.7393 (p0) cc_final: 0.7171 (t0) REVERT: F 345 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8065 (pptt) outliers start: 58 outliers final: 49 residues processed: 224 average time/residue: 0.2409 time to fit residues: 79.1875 Evaluate side-chains 231 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 178 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 312 ARG Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain A residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 337 HIS D 79 HIS F 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.087526 restraints weight = 21656.965| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.39 r_work: 0.3062 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2977 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= 0.171 Angle : 0.585 11.713 17550 Z= 0.284 Chirality : 0.040 0.205 2045 Planarity : 0.003 0.036 2241 Dihedral : 9.801 83.679 1982 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.18 % Allowed : 26.16 % Favored : 69.66 % 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: 0.02 (0.22), residues: 1648 helix: 1.25 (0.20), residues: 797 sheet: -0.84 (0.42), residues: 146 loop : -1.25 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.009 0.001 HIS F 79 PHE 0.012 0.001 PHE D 351 TYR 0.005 0.001 TYR C 167 ARG 0.007 0.000 ARG D 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2959.58 seconds wall clock time: 54 minutes 16.75 seconds (3256.75 seconds total)