Starting phenix.real_space_refine on Sat Jan 20 03:48:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upt_26675/01_2024/7upt_26675_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upt_26675/01_2024/7upt_26675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upt_26675/01_2024/7upt_26675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upt_26675/01_2024/7upt_26675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upt_26675/01_2024/7upt_26675_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upt_26675/01_2024/7upt_26675_updated.pdb" } resolution = 3.5 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= 0.052 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 17 5.49 5 Mg 5 5.21 5 S 93 5.16 5 C 8512 2.51 5 N 2386 2.21 5 O 2554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 192": "OD1" <-> "OD2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 199": "NH1" <-> "NH2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "F ARG 329": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13567 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2148 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2343 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "C" 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: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2318 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2311 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Chain breaks: 1 Chain: "F" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1853 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 4 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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: "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: "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: "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: "F" 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} Time building chain proxies: 7.31, per 1000 atoms: 0.54 Number of scatterers: 13567 At special positions: 0 Unit cell: (96.512, 130.624, 138.112, 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 93 16.00 P 17 15.00 Mg 5 11.99 O 2554 8.00 N 2386 7.00 C 8512 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3266 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 8 sheets defined 49.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 72 through 79 removed outlier: 4.517A pdb=" N HIS A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 108 through 111 No H-bonds generated for 'chain 'A' and resid 108 through 111' Processing helix chain 'A' and resid 114 through 117 No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 194 through 197 No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 207 through 221 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 262 through 273 removed outlier: 4.563A pdb=" N GLU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.551A pdb=" N LYS A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'B' and resid 48 through 62 removed outlier: 3.664A pdb=" N GLN B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 79 removed outlier: 4.051A pdb=" N ALA B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 111 removed outlier: 4.333A pdb=" N LEU B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 159 through 162 No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 170 through 183 removed outlier: 3.887A 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 207 through 221 removed outlier: 3.694A pdb=" N ASP B 221 " --> pdb=" O MET B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 262 through 274 Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.852A pdb=" N ALA B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 284 through 290' Processing helix chain 'B' and resid 296 through 314 Processing helix chain 'B' and resid 334 through 347 removed outlier: 3.868A pdb=" N LYS B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 62 removed outlier: 3.808A pdb=" N ALA C 51 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 62 " --> pdb=" O MET C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 79 removed outlier: 4.974A 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 98 through 106 Processing helix chain 'C' and resid 109 through 112 No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 139 through 149 removed outlier: 3.815A pdb=" N ALA C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 169 through 183 removed outlier: 3.748A 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 221 removed outlier: 3.616A pdb=" N ASP C 221 " --> pdb=" O MET C 217 " (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 247 through 250 No H-bonds generated for 'chain 'C' and resid 247 through 250' Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 296 through 316 removed outlier: 3.941A pdb=" N GLU C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR C 314 " --> pdb=" O CYS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 347 removed outlier: 3.540A pdb=" N GLU C 341 " --> pdb=" O HIS C 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 4.076A pdb=" N LYS D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 79 removed outlier: 3.584A pdb=" N ALA D 78 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) 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 97 through 111 removed outlier: 4.031A pdb=" N LEU D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 169 through 183 removed outlier: 3.652A pdb=" N ALA D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.876A 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 221 removed outlier: 3.537A pdb=" N MET D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 262 through 272 Processing helix chain 'D' and resid 284 through 290 removed outlier: 3.832A pdb=" N GLU D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 312 removed outlier: 3.513A pdb=" N LEU D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 349 Processing helix chain 'E' and resid 47 through 61 Processing helix chain 'E' and resid 72 through 79 removed outlier: 3.615A pdb=" N ALA E 78 " --> pdb=" O MET E 74 " (cutoff:3.500A) removed outlier: 4.828A 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 97 through 111 Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 159 through 162 No H-bonds generated for 'chain 'E' and resid 159 through 162' Processing helix chain 'E' and resid 169 through 183 removed outlier: 3.866A 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 221 removed outlier: 3.534A pdb=" N LYS E 213 " --> pdb=" O THR E 209 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP E 221 " --> pdb=" O MET E 217 " (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 272 Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 296 through 312 Processing helix chain 'E' and resid 334 through 346 Processing helix chain 'F' and resid 72 through 79 removed outlier: 4.520A pdb=" N HIS F 79 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'F' and resid 97 through 106 removed outlier: 3.723A pdb=" N LYS F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 111 No H-bonds generated for 'chain 'F' and resid 108 through 111' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 170 through 183 removed outlier: 4.125A pdb=" N PHE F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 246 through 250 removed outlier: 3.885A pdb=" N ARG F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 246 through 250' Processing helix chain 'F' and resid 262 through 272 removed outlier: 3.637A pdb=" N LEU F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 272 " --> pdb=" O ILE F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 296 through 315 removed outlier: 3.529A pdb=" N CYS F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 347 removed outlier: 3.645A pdb=" N LYS F 345 " --> pdb=" O GLU F 341 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.735A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 155 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 253 through 257 removed outlier: 6.811A pdb=" N SER B 187 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N MET B 234 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 189 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA B 236 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 191 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N PHE B 190 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 129 through 133 removed outlier: 6.862A pdb=" N THR C 253 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N TYR C 132 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE C 255 " --> pdb=" O TYR C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.810A pdb=" N ILE C 232 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= F, first strand: chain 'D' and resid 154 through 156 removed outlier: 5.894A pdb=" N ILE D 188 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE D 232 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE D 191 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 253 through 256 removed outlier: 6.321A pdb=" N SER E 187 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N MET E 234 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE E 189 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA E 236 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE E 191 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE E 190 " --> pdb=" O ARG E 153 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ASP E 192 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 253 through 257 removed outlier: 3.509A pdb=" N GLY F 235 " --> pdb=" O VAL F 129 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1323 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: 3.47 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4468 1.34 - 1.46: 2690 1.46 - 1.58: 6445 1.58 - 1.70: 28 1.70 - 1.81: 157 Bond restraints: 13788 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.48e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 bond pdb=" C4 ATP F 602 " pdb=" C5 ATP F 602 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.41e+01 ... (remaining 13783 not shown) Histogram of bond angle deviations from ideal: 100.17 - 107.39: 554 107.39 - 114.60: 8309 114.60 - 121.82: 6906 121.82 - 129.04: 2755 129.04 - 136.25: 95 Bond angle restraints: 18619 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 119.66 20.21 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 119.75 20.12 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 119.77 20.10 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 119.98 19.89 1.00e+00 1.00e+00 3.95e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 120.00 19.87 1.00e+00 1.00e+00 3.95e+02 ... (remaining 18614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 7471 21.67 - 43.34: 886 43.34 - 65.02: 262 65.02 - 86.69: 34 86.69 - 108.36: 5 Dihedral angle restraints: 8658 sinusoidal: 3682 harmonic: 4976 Sorted by residual: dihedral pdb=" CA HIS C 227 " pdb=" C HIS C 227 " pdb=" N SER C 228 " pdb=" CA SER C 228 " ideal model delta harmonic sigma weight residual 180.00 147.88 32.12 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" C2' ADP A 501 " pdb=" C1' ADP A 501 " pdb=" N9 ADP A 501 " pdb=" C4 ADP A 501 " ideal model delta sinusoidal sigma weight residual 91.55 -16.81 108.36 1 2.00e+01 2.50e-03 3.16e+01 dihedral pdb=" CA CYS D 137 " pdb=" C CYS D 137 " pdb=" N GLY D 138 " pdb=" CA GLY D 138 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 8655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 2114 0.344 - 0.688: 0 0.688 - 1.032: 0 1.032 - 1.376: 0 1.376 - 1.720: 13 Chirality restraints: 2127 Sorted by residual: chirality pdb=" CG LEU F 243 " pdb=" CB LEU F 243 " pdb=" CD1 LEU F 243 " pdb=" CD2 LEU F 243 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.39e+01 chirality pdb=" CG LEU F 271 " pdb=" CB LEU F 271 " pdb=" CD1 LEU F 271 " pdb=" CD2 LEU F 271 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU C 141 " pdb=" CB LEU C 141 " pdb=" CD1 LEU C 141 " pdb=" CD2 LEU C 141 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.26e+01 ... (remaining 2124 not shown) Planarity restraints: 2349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 56 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C GLU D 56 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU D 56 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS D 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 109 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO B 110 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 109 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO F 110 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO F 110 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 110 " -0.021 5.00e-02 4.00e+02 ... (remaining 2346 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 165 2.54 - 3.13: 11799 3.13 - 3.72: 22103 3.72 - 4.31: 28539 4.31 - 4.90: 46638 Nonbonded interactions: 109244 Sorted by model distance: nonbonded pdb=" O LEU E 184 " pdb=" OG SER E 187 " model vdw 1.944 2.440 nonbonded pdb="MG MG C 601 " pdb=" O3B ATP C 602 " model vdw 1.953 2.170 nonbonded pdb=" OG1 THR C 140 " pdb="MG MG C 601 " model vdw 1.953 2.170 nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 601 " model vdw 1.955 2.170 nonbonded pdb=" OG1 THR E 140 " pdb="MG MG E 502 " model vdw 1.964 2.170 ... (remaining 109239 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' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 314 or resid 328 through 351)) selection = (chain 'B' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 314 or resid 328 through 351)) selection = (chain 'C' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 314 or resid 328 through 351)) selection = (chain 'D' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 314 or resid 328 through 351)) selection = (chain 'E' and (resid 69 through 112 or resid 128 through 197 or resid 210 throu \ gh 220 or resid 230 through 351)) selection = (chain 'F' and (resid 69 through 314 or resid 328 through 351)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 7.420 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.180 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 0.080 13788 Z= 0.271 Angle : 0.949 20.207 18619 Z= 0.655 Chirality : 0.132 1.720 2127 Planarity : 0.003 0.041 2349 Dihedral : 19.591 108.360 5392 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.60 % Rotamer: Outliers : 11.28 % Allowed : 22.89 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -3.04 (0.18), residues: 1662 helix: -1.62 (0.16), residues: 804 sheet: -2.39 (0.38), residues: 154 loop : -2.27 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 220 HIS 0.003 0.000 HIS D 227 PHE 0.009 0.001 PHE B 154 TYR 0.004 0.000 TYR F 132 ARG 0.003 0.000 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 253 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7847 (m-70) cc_final: 0.7441 (m170) REVERT: A 157 LEU cc_start: 0.8957 (tp) cc_final: 0.8591 (tt) REVERT: A 184 LEU cc_start: 0.9262 (tp) cc_final: 0.8939 (tp) REVERT: A 258 ASN cc_start: 0.7451 (t0) cc_final: 0.6554 (p0) REVERT: A 298 ASP cc_start: 0.8412 (m-30) cc_final: 0.8091 (m-30) REVERT: B 54 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 66 ASN cc_start: 0.8495 (m110) cc_final: 0.8242 (t0) REVERT: B 71 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7796 (tp30) REVERT: B 312 ARG cc_start: 0.8785 (tmt90) cc_final: 0.8402 (tmm-80) REVERT: C 59 MET cc_start: 0.8651 (ttp) cc_final: 0.8381 (tmm) REVERT: C 220 TRP cc_start: 0.8307 (t60) cc_final: 0.8085 (t60) REVERT: C 343 MET cc_start: 0.8794 (tpt) cc_final: 0.8526 (tpp) REVERT: D 47 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.5435 (pp30) REVERT: E 61 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8721 (tm-30) REVERT: E 132 TYR cc_start: 0.8351 (p90) cc_final: 0.7768 (p90) REVERT: E 203 SER cc_start: 0.8190 (t) cc_final: 0.7875 (p) REVERT: F 85 ASN cc_start: 0.9531 (m-40) cc_final: 0.9266 (m-40) REVERT: F 248 MET cc_start: 0.8175 (ttt) cc_final: 0.7972 (ttt) REVERT: F 249 ARG cc_start: 0.8346 (mmp80) cc_final: 0.8137 (mtt-85) REVERT: F 280 ARG cc_start: 0.8780 (tpp-160) cc_final: 0.8099 (tpm170) REVERT: F 281 HIS cc_start: 0.8272 (m170) cc_final: 0.7436 (t70) REVERT: F 311 VAL cc_start: 0.9332 (t) cc_final: 0.9077 (t) REVERT: F 342 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7794 (tmtt) outliers start: 166 outliers final: 107 residues processed: 404 average time/residue: 0.3145 time to fit residues: 173.0831 Evaluate side-chains 290 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 181 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 335 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 289 GLN A 337 HIS B 66 ASN B 206 HIS ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN C 230 GLN D 193 GLN D 227 HIS E 115 HIS E 215 GLN E 238 ASN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN F 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 13788 Z= 0.436 Angle : 0.766 13.172 18619 Z= 0.382 Chirality : 0.046 0.292 2127 Planarity : 0.005 0.052 2349 Dihedral : 15.380 119.066 2245 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.48 % Favored : 91.40 % Rotamer: Outliers : 12.36 % Allowed : 24.52 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.20), residues: 1662 helix: -0.78 (0.17), residues: 818 sheet: -2.01 (0.37), residues: 181 loop : -1.78 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 220 HIS 0.003 0.001 HIS E 281 PHE 0.022 0.002 PHE D 154 TYR 0.010 0.002 TYR F 132 ARG 0.007 0.001 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 174 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8715 (ptmm) REVERT: A 224 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: A 258 ASN cc_start: 0.7625 (t0) cc_final: 0.6649 (p0) REVERT: A 263 LYS cc_start: 0.9241 (tppt) cc_final: 0.9028 (mptt) REVERT: A 343 MET cc_start: 0.2851 (OUTLIER) cc_final: 0.2188 (mmm) REVERT: B 65 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6272 (pttm) REVERT: B 66 ASN cc_start: 0.8458 (m-40) cc_final: 0.8258 (t0) REVERT: B 71 GLU cc_start: 0.8679 (mm-30) cc_final: 0.7935 (tp30) REVERT: B 72 TYR cc_start: 0.8293 (m-80) cc_final: 0.7603 (m-10) REVERT: B 96 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8039 (pp) REVERT: B 121 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8266 (ttp-170) REVERT: B 312 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8388 (tpt90) REVERT: C 248 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7935 (tmm) REVERT: C 313 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: D 47 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.5600 (pp30) REVERT: D 74 MET cc_start: 0.8041 (tpp) cc_final: 0.7770 (tpp) REVERT: D 96 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8013 (pp) REVERT: E 61 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8620 (tm-30) REVERT: E 203 SER cc_start: 0.8325 (t) cc_final: 0.8026 (p) REVERT: E 343 MET cc_start: 0.8601 (mmm) cc_final: 0.8385 (mmt) REVERT: F 249 ARG cc_start: 0.8429 (mmp80) cc_final: 0.8143 (mtm-85) REVERT: F 280 ARG cc_start: 0.8774 (tpp-160) cc_final: 0.8071 (tpm170) REVERT: F 281 HIS cc_start: 0.8315 (m170) cc_final: 0.7451 (t70) REVERT: F 342 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7807 (tmtt) outliers start: 182 outliers final: 128 residues processed: 334 average time/residue: 0.2707 time to fit residues: 127.9196 Evaluate side-chains 289 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 149 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 303 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN E 264 GLN F 79 HIS F 158 GLN ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13788 Z= 0.218 Angle : 0.670 11.491 18619 Z= 0.326 Chirality : 0.043 0.228 2127 Planarity : 0.004 0.051 2349 Dihedral : 14.337 119.741 2193 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 9.85 % Allowed : 25.95 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.21), residues: 1662 helix: -0.14 (0.18), residues: 810 sheet: -1.73 (0.38), residues: 179 loop : -1.44 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 90 HIS 0.008 0.001 HIS A 79 PHE 0.013 0.001 PHE D 154 TYR 0.006 0.001 TYR E 314 ARG 0.004 0.000 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 168 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.7635 (m-70) cc_final: 0.6590 (m-70) REVERT: A 158 GLN cc_start: 0.8782 (mt0) cc_final: 0.8342 (mt0) REVERT: A 211 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8375 (tmt) REVERT: A 224 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: A 258 ASN cc_start: 0.7396 (t0) cc_final: 0.6688 (p0) REVERT: B 66 ASN cc_start: 0.8452 (m-40) cc_final: 0.8182 (t0) REVERT: B 71 GLU cc_start: 0.8632 (mm-30) cc_final: 0.7879 (tp30) REVERT: B 72 TYR cc_start: 0.8278 (m-80) cc_final: 0.7721 (m-10) REVERT: B 96 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.7921 (pp) REVERT: B 121 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8151 (ttp-170) REVERT: B 312 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8395 (tmm-80) REVERT: C 59 MET cc_start: 0.8238 (tmm) cc_final: 0.7683 (tmm) REVERT: C 248 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7851 (tmm) REVERT: D 47 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.5500 (pp30) REVERT: D 96 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7672 (pp) REVERT: D 234 MET cc_start: 0.7941 (ptm) cc_final: 0.7710 (ptm) REVERT: D 248 MET cc_start: 0.8644 (tpp) cc_final: 0.8370 (ttp) REVERT: D 274 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8981 (mtpp) REVERT: E 61 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: E 266 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8518 (tm-30) REVERT: F 248 MET cc_start: 0.8393 (ttt) cc_final: 0.7960 (ttt) REVERT: F 249 ARG cc_start: 0.8344 (mmp80) cc_final: 0.7902 (mtm-85) REVERT: F 281 HIS cc_start: 0.8330 (m170) cc_final: 0.7507 (t70) REVERT: F 342 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7852 (tmtt) outliers start: 145 outliers final: 107 residues processed: 293 average time/residue: 0.2583 time to fit residues: 108.5897 Evaluate side-chains 276 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 158 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG 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 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN D 61 GLN E 256 HIS F 79 HIS ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13788 Z= 0.229 Angle : 0.646 11.097 18619 Z= 0.312 Chirality : 0.042 0.188 2127 Planarity : 0.004 0.051 2349 Dihedral : 13.926 122.874 2165 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.18 % Favored : 91.76 % Rotamer: Outliers : 10.80 % Allowed : 25.27 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -1.08 (0.21), residues: 1662 helix: 0.09 (0.18), residues: 811 sheet: -1.59 (0.38), residues: 181 loop : -1.35 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 220 HIS 0.003 0.001 HIS B 79 PHE 0.013 0.001 PHE D 154 TYR 0.007 0.001 TYR E 72 ARG 0.004 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 170 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8303 (tmt) REVERT: A 224 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: A 258 ASN cc_start: 0.7631 (t0) cc_final: 0.6878 (p0) REVERT: B 65 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6068 (pttm) REVERT: B 71 GLU cc_start: 0.8666 (mm-30) cc_final: 0.7910 (tp30) REVERT: B 72 TYR cc_start: 0.8322 (m-80) cc_final: 0.7877 (m-10) REVERT: B 96 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7934 (pp) REVERT: B 121 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8165 (ttp-170) REVERT: B 185 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: B 312 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8234 (tmm-80) REVERT: C 59 MET cc_start: 0.8225 (tmm) cc_final: 0.7827 (tmm) REVERT: C 248 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7755 (tmm) REVERT: D 47 GLN cc_start: 0.6519 (OUTLIER) cc_final: 0.5463 (pp30) REVERT: D 96 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7771 (pp) REVERT: D 234 MET cc_start: 0.7954 (ptm) cc_final: 0.7748 (ptm) REVERT: E 61 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: E 266 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8482 (tm-30) REVERT: F 166 TRP cc_start: 0.6520 (t-100) cc_final: 0.6226 (t-100) REVERT: F 249 ARG cc_start: 0.8362 (mmp80) cc_final: 0.7930 (mtm-85) REVERT: F 281 HIS cc_start: 0.8329 (m170) cc_final: 0.7528 (t70) REVERT: F 342 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7848 (tmtt) outliers start: 159 outliers final: 110 residues processed: 312 average time/residue: 0.2746 time to fit residues: 123.8330 Evaluate side-chains 276 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 154 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 144 optimal weight: 50.0000 chunk 40 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 230 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS D 215 GLN D 333 GLN E 289 GLN F 79 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13788 Z= 0.402 Angle : 0.720 9.851 18619 Z= 0.355 Chirality : 0.044 0.147 2127 Planarity : 0.005 0.052 2349 Dihedral : 13.762 129.965 2138 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.15 % Favored : 90.79 % Rotamer: Outliers : 12.09 % Allowed : 25.00 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1662 helix: -0.05 (0.18), residues: 821 sheet: -1.64 (0.39), residues: 183 loop : -1.47 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 220 HIS 0.005 0.001 HIS E 87 PHE 0.022 0.002 PHE D 154 TYR 0.010 0.001 TYR E 72 ARG 0.005 0.001 ARG F 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 150 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8215 (tmt) REVERT: A 212 MET cc_start: 0.9139 (tpp) cc_final: 0.8929 (tpp) REVERT: A 224 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: A 258 ASN cc_start: 0.7662 (t0) cc_final: 0.6792 (p0) REVERT: B 65 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6111 (pttm) REVERT: B 71 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8070 (tp30) REVERT: B 72 TYR cc_start: 0.8303 (m-80) cc_final: 0.8073 (m-10) REVERT: B 96 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8008 (pp) REVERT: B 121 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8141 (ttp-170) REVERT: B 185 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: B 248 MET cc_start: 0.8857 (tpp) cc_final: 0.8529 (tpp) REVERT: B 275 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.7803 (t0) REVERT: C 59 MET cc_start: 0.8247 (tmm) cc_final: 0.7712 (tmm) REVERT: C 248 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7820 (tmm) REVERT: C 313 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: D 74 MET cc_start: 0.8319 (tpp) cc_final: 0.7973 (mpp) REVERT: D 96 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7891 (pp) REVERT: D 184 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8754 (pp) REVERT: D 333 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: E 250 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.5708 (mpt90) REVERT: E 266 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: F 87 HIS cc_start: 0.7694 (m90) cc_final: 0.6725 (t-170) REVERT: F 249 ARG cc_start: 0.8287 (mmp80) cc_final: 0.7861 (mtm-85) REVERT: F 342 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7861 (tmtt) outliers start: 178 outliers final: 141 residues processed: 303 average time/residue: 0.2431 time to fit residues: 107.5909 Evaluate side-chains 301 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 146 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 TYR Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 161 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS F 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13788 Z= 0.190 Angle : 0.642 10.474 18619 Z= 0.310 Chirality : 0.042 0.262 2127 Planarity : 0.004 0.052 2349 Dihedral : 13.351 125.988 2131 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.30 % Favored : 91.64 % Rotamer: Outliers : 9.51 % Allowed : 27.38 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.93 (0.21), residues: 1662 helix: 0.23 (0.18), residues: 820 sheet: -1.50 (0.39), residues: 180 loop : -1.33 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.006 0.001 HIS F 79 PHE 0.013 0.001 PHE D 154 TYR 0.008 0.001 TYR F 72 ARG 0.003 0.000 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 166 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.8225 (m90) cc_final: 0.8020 (m170) REVERT: A 211 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8221 (tmt) REVERT: A 212 MET cc_start: 0.9149 (tpp) cc_final: 0.8934 (tpp) REVERT: A 224 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: A 258 ASN cc_start: 0.7656 (t0) cc_final: 0.6904 (p0) REVERT: A 343 MET cc_start: 0.3196 (OUTLIER) cc_final: 0.2501 (mmm) REVERT: B 71 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8074 (tp30) REVERT: B 72 TYR cc_start: 0.8302 (m-80) cc_final: 0.8025 (m-10) REVERT: B 96 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7964 (pp) REVERT: B 104 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8136 (ptpp) REVERT: B 185 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: B 312 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8440 (tmm-80) REVERT: C 59 MET cc_start: 0.8100 (tmm) cc_final: 0.7830 (tmm) REVERT: C 207 GLU cc_start: 0.8661 (pp20) cc_final: 0.8417 (pp20) REVERT: C 248 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7794 (tmm) REVERT: D 96 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7666 (pp) REVERT: D 197 PHE cc_start: 0.8690 (t80) cc_final: 0.8267 (t80) REVERT: E 61 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: E 250 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5767 (mpt90) REVERT: E 266 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8495 (tm-30) REVERT: F 86 MET cc_start: 0.8930 (ptp) cc_final: 0.8599 (ptp) REVERT: F 87 HIS cc_start: 0.7719 (m90) cc_final: 0.6892 (t70) REVERT: F 166 TRP cc_start: 0.6556 (t-100) cc_final: 0.6243 (t-100) REVERT: F 234 MET cc_start: 0.6733 (mpp) cc_final: 0.6495 (mpp) REVERT: F 249 ARG cc_start: 0.8247 (mmp80) cc_final: 0.7775 (mtm-85) REVERT: F 281 HIS cc_start: 0.8411 (m90) cc_final: 0.7561 (t70) REVERT: F 342 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7833 (tmtt) outliers start: 140 outliers final: 105 residues processed: 287 average time/residue: 0.2502 time to fit residues: 104.3829 Evaluate side-chains 276 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 159 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN D 333 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS F 193 GLN ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13788 Z= 0.238 Angle : 0.657 10.987 18619 Z= 0.315 Chirality : 0.042 0.167 2127 Planarity : 0.004 0.052 2349 Dihedral : 13.155 125.613 2118 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.60 % Favored : 91.34 % Rotamer: Outliers : 9.92 % Allowed : 27.24 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.82 (0.21), residues: 1662 helix: 0.26 (0.18), residues: 828 sheet: -1.34 (0.40), residues: 181 loop : -1.24 (0.26), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.009 0.001 HIS F 79 PHE 0.017 0.001 PHE D 154 TYR 0.020 0.001 TYR A 72 ARG 0.003 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 156 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8195 (tmt) REVERT: A 212 MET cc_start: 0.9130 (tpp) cc_final: 0.8902 (tpp) REVERT: A 224 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: A 258 ASN cc_start: 0.7684 (t0) cc_final: 0.6995 (p0) REVERT: B 65 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.5861 (pttm) REVERT: B 71 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8040 (tp30) REVERT: B 96 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.7946 (pp) REVERT: B 104 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8142 (ptpp) REVERT: B 121 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8033 (ttp-170) REVERT: B 153 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6941 (mmt90) REVERT: B 185 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: B 248 MET cc_start: 0.8812 (tpp) cc_final: 0.8363 (tpp) REVERT: B 312 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8461 (tmm-80) REVERT: C 53 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8910 (mmmt) REVERT: C 59 MET cc_start: 0.8020 (tmm) cc_final: 0.7809 (tmm) REVERT: C 207 GLU cc_start: 0.8691 (pp20) cc_final: 0.8429 (pp20) REVERT: C 248 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7795 (tmm) REVERT: D 74 MET cc_start: 0.8157 (tpp) cc_final: 0.7893 (mpp) REVERT: D 96 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7711 (pp) REVERT: D 333 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: E 266 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: F 166 TRP cc_start: 0.6578 (t-100) cc_final: 0.6263 (t-100) REVERT: F 281 HIS cc_start: 0.8375 (m90) cc_final: 0.7611 (t70) REVERT: F 342 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7850 (tmtt) outliers start: 146 outliers final: 114 residues processed: 284 average time/residue: 0.2468 time to fit residues: 102.6586 Evaluate side-chains 278 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 150 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 79 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13788 Z= 0.178 Angle : 0.647 10.530 18619 Z= 0.308 Chirality : 0.041 0.153 2127 Planarity : 0.004 0.055 2349 Dihedral : 12.771 123.046 2110 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 8.22 % Allowed : 29.69 % Favored : 62.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.72 (0.21), residues: 1662 helix: 0.36 (0.18), residues: 824 sheet: -1.27 (0.40), residues: 182 loop : -1.22 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 166 HIS 0.005 0.000 HIS D 227 PHE 0.014 0.001 PHE D 154 TYR 0.007 0.001 TYR A 72 ARG 0.006 0.000 ARG E 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 161 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8213 (tmt) REVERT: A 224 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: A 258 ASN cc_start: 0.7592 (t0) cc_final: 0.6986 (p0) REVERT: A 343 MET cc_start: 0.3231 (OUTLIER) cc_final: 0.2555 (mmm) REVERT: B 71 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7818 (tp30) REVERT: B 96 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.7948 (pp) REVERT: B 185 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: B 248 MET cc_start: 0.8773 (tpp) cc_final: 0.8260 (tpp) REVERT: B 312 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8481 (tmm-80) REVERT: C 66 ASN cc_start: 0.8894 (p0) cc_final: 0.8668 (p0) REVERT: C 207 GLU cc_start: 0.8666 (pp20) cc_final: 0.8419 (pp20) REVERT: C 248 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7768 (tmm) REVERT: C 276 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: D 96 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7644 (pp) REVERT: E 61 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8525 (tm-30) REVERT: E 217 MET cc_start: 0.8355 (mmm) cc_final: 0.8109 (mmp) REVERT: F 166 TRP cc_start: 0.6543 (t-100) cc_final: 0.6230 (t-100) REVERT: F 234 MET cc_start: 0.6702 (mpp) cc_final: 0.6465 (mpp) REVERT: F 281 HIS cc_start: 0.8388 (m90) cc_final: 0.7668 (t70) REVERT: F 342 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7811 (tmtt) outliers start: 121 outliers final: 99 residues processed: 264 average time/residue: 0.2377 time to fit residues: 92.8165 Evaluate side-chains 264 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 155 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 TYR Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 277 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 117 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13788 Z= 0.171 Angle : 0.673 13.586 18619 Z= 0.314 Chirality : 0.041 0.146 2127 Planarity : 0.004 0.055 2349 Dihedral : 12.332 121.543 2094 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 7.95 % Allowed : 29.89 % Favored : 62.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.61 (0.21), residues: 1662 helix: 0.44 (0.18), residues: 822 sheet: -1.14 (0.40), residues: 182 loop : -1.18 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 90 HIS 0.005 0.000 HIS D 227 PHE 0.013 0.001 PHE D 154 TYR 0.008 0.001 TYR F 72 ARG 0.005 0.000 ARG E 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 161 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8164 (tmt) REVERT: A 224 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: A 258 ASN cc_start: 0.7572 (t0) cc_final: 0.7023 (p0) REVERT: A 343 MET cc_start: 0.3228 (OUTLIER) cc_final: 0.2566 (mmm) REVERT: B 71 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7828 (tp30) REVERT: B 96 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7958 (pp) REVERT: B 153 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7411 (mmt90) REVERT: B 185 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: B 248 MET cc_start: 0.8778 (tpp) cc_final: 0.8187 (tpp) REVERT: B 312 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8487 (tmm-80) REVERT: C 207 GLU cc_start: 0.8687 (pp20) cc_final: 0.8443 (pp20) REVERT: C 248 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7718 (tmm) REVERT: D 74 MET cc_start: 0.8090 (tpp) cc_final: 0.7833 (mpp) REVERT: D 96 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7535 (pp) REVERT: E 61 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8666 (tm-30) REVERT: E 217 MET cc_start: 0.8358 (mmm) cc_final: 0.8110 (mmp) REVERT: E 266 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8420 (tm-30) REVERT: E 341 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8740 (mm-30) REVERT: F 166 TRP cc_start: 0.6470 (t-100) cc_final: 0.6161 (t-100) REVERT: F 234 MET cc_start: 0.6704 (mpp) cc_final: 0.6449 (mpp) REVERT: F 281 HIS cc_start: 0.8420 (m90) cc_final: 0.7744 (t70) REVERT: F 342 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7822 (tmtt) outliers start: 117 outliers final: 93 residues processed: 259 average time/residue: 0.2573 time to fit residues: 100.0179 Evaluate side-chains 261 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 156 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS B 238 ASN ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS D 238 ASN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13788 Z= 0.306 Angle : 0.704 13.083 18619 Z= 0.338 Chirality : 0.043 0.267 2127 Planarity : 0.004 0.056 2349 Dihedral : 12.435 124.393 2080 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.09 % Favored : 90.85 % Rotamer: Outliers : 8.15 % Allowed : 29.89 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.68 (0.22), residues: 1662 helix: 0.37 (0.19), residues: 825 sheet: -1.16 (0.40), residues: 183 loop : -1.21 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 90 HIS 0.004 0.001 HIS D 227 PHE 0.020 0.002 PHE D 154 TYR 0.006 0.001 TYR A 72 ARG 0.007 0.000 ARG E 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 154 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 HIS cc_start: 0.8294 (m90) cc_final: 0.7321 (m-70) REVERT: A 211 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8158 (tmt) REVERT: A 224 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: A 258 ASN cc_start: 0.7630 (t0) cc_final: 0.6955 (p0) REVERT: B 71 GLU cc_start: 0.8720 (mm-30) cc_final: 0.7969 (tp30) REVERT: B 96 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7926 (pp) REVERT: B 153 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7696 (mmt90) REVERT: B 185 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: B 248 MET cc_start: 0.8787 (tpp) cc_final: 0.8212 (tpp) REVERT: B 312 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8480 (tmm-80) REVERT: C 207 GLU cc_start: 0.8708 (pp20) cc_final: 0.8446 (pp20) REVERT: C 248 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7742 (tmm) REVERT: D 96 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7751 (pp) REVERT: E 61 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: E 217 MET cc_start: 0.8359 (mmm) cc_final: 0.8105 (mmp) REVERT: E 266 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: F 166 TRP cc_start: 0.6564 (t-100) cc_final: 0.6262 (t-100) REVERT: F 249 ARG cc_start: 0.8160 (mmp80) cc_final: 0.7740 (ttm-80) REVERT: F 281 HIS cc_start: 0.8431 (m90) cc_final: 0.7723 (t70) REVERT: F 342 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7842 (tmtt) outliers start: 120 outliers final: 102 residues processed: 255 average time/residue: 0.2332 time to fit residues: 88.7977 Evaluate side-chains 262 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 150 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 TYR Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLU Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 TYR Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 301 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** F 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068148 restraints weight = 39702.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.070804 restraints weight = 18225.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072593 restraints weight = 11466.373| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13788 Z= 0.254 Angle : 0.698 13.173 18619 Z= 0.331 Chirality : 0.042 0.262 2127 Planarity : 0.004 0.055 2349 Dihedral : 12.409 123.994 2080 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.60 % Favored : 91.34 % Rotamer: Outliers : 8.49 % Allowed : 30.03 % Favored : 61.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: -0.71 (0.22), residues: 1662 helix: 0.35 (0.18), residues: 826 sheet: -1.19 (0.40), residues: 183 loop : -1.22 (0.26), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 90 HIS 0.004 0.001 HIS D 227 PHE 0.019 0.001 PHE E 190 TYR 0.008 0.001 TYR F 72 ARG 0.008 0.000 ARG D 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3136.89 seconds wall clock time: 57 minutes 47.64 seconds (3467.64 seconds total)