Starting phenix.real_space_refine on Thu Feb 15 19:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe0_20320/02_2024/6pe0_20320_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe0_20320/02_2024/6pe0_20320.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/6pe0_20320/02_2024/6pe0_20320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe0_20320/02_2024/6pe0_20320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe0_20320/02_2024/6pe0_20320_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe0_20320/02_2024/6pe0_20320_neut_trim_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= 0.006 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 59 5.16 5 C 8268 2.51 5 N 2349 2.21 5 O 2490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 93": "OE1" <-> "OE2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F ARG 264": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F ARG 303": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 337": "NH1" <-> "NH2" Residue "F ARG 341": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 303": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "D ARG 303": "NH1" <-> "NH2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E ARG 274": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E ARG 303": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 337": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13186 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1914 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain breaks: 1 Chain: "A" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2050 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 245} Chain breaks: 4 Chain: "B" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2209 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2327 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2293 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 275} Chain breaks: 1 Chain: "E" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2183 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 1 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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} Time building chain proxies: 7.13, per 1000 atoms: 0.54 Number of scatterers: 13186 At special positions: 0 Unit cell: (86.838, 139.788, 135.552, 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 59 16.00 P 15 15.00 Mg 5 11.99 O 2490 8.00 N 2349 7.00 C 8268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.2 seconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 6 sheets defined 42.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'F' and resid 94 through 99 removed outlier: 5.313A pdb=" N LEU F 98 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 158 through 170 removed outlier: 4.424A pdb=" N MET F 162 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU F 163 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA F 168 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 183 Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.573A pdb=" N PHE F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 241 removed outlier: 3.715A pdb=" N MET F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 removed outlier: 4.277A pdb=" N ARG F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 299 removed outlier: 3.713A pdb=" N ARG F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 315 removed outlier: 3.644A pdb=" N VAL F 315 " --> pdb=" O ILE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 326 Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 119 through 131 removed outlier: 4.739A pdb=" N ILE A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TYR A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 193 through 204 Processing helix chain 'A' and resid 215 through 218 No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.644A pdb=" N MET A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.929A pdb=" N ARG A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 309 through 312 No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 321 through 345 removed outlier: 3.700A pdb=" N LYS A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Proline residue: A 335 - end of helix removed outlier: 4.284A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 64 Processing helix chain 'B' and resid 96 through 99 removed outlier: 3.816A pdb=" N GLU B 99 " --> pdb=" O VAL B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.905A pdb=" N VAL B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 242 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.746A pdb=" N ARG B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 323 through 338 removed outlier: 3.591A pdb=" N CYS B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 341 through 344 No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'C' and resid 45 through 63 removed outlier: 3.724A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 removed outlier: 3.857A pdb=" N VAL C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 99' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 118 through 131 removed outlier: 5.612A pdb=" N TYR C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Proline residue: C 130 - end of helix Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 160 through 170 removed outlier: 3.738A pdb=" N ALA C 166 " --> pdb=" O MET C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 191 through 202 removed outlier: 3.705A pdb=" N PHE C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 241 removed outlier: 4.311A pdb=" N MET C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 270 through 273 No H-bonds generated for 'chain 'C' and resid 270 through 273' Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.972A pdb=" N ARG C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 315 removed outlier: 3.589A pdb=" N ARG C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 332 Processing helix chain 'C' and resid 334 through 345 removed outlier: 4.464A pdb=" N ALA C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 63 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.518A pdb=" N LEU D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 117 through 124 removed outlier: 3.605A pdb=" N GLU D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 removed outlier: 3.736A pdb=" N ALA D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.643A pdb=" N PHE D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 218 No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.858A pdb=" N PHE D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 removed outlier: 3.664A pdb=" N GLU D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'D' and resid 321 through 342 Proline residue: D 335 - end of helix removed outlier: 4.072A pdb=" N GLN D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 63 Processing helix chain 'E' and resid 93 through 99 removed outlier: 4.558A pdb=" N LEU E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 removed outlier: 3.727A pdb=" N LYS E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 131 No H-bonds generated for 'chain 'E' and resid 128 through 131' Processing helix chain 'E' and resid 134 through 138 Processing helix chain 'E' and resid 160 through 169 removed outlier: 3.939A pdb=" N ALA E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 183 No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 190 through 204 removed outlier: 3.572A pdb=" N LYS E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 228 through 231 No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 233 through 241 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.514A pdb=" N ARG E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'E' and resid 321 through 341 removed outlier: 3.984A pdb=" N MET E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Proline residue: E 335 - end of helix removed outlier: 4.091A pdb=" N GLU E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 339 " --> pdb=" O PRO E 335 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE E 340 " --> pdb=" O MET E 336 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG E 341 " --> pdb=" O ARG E 337 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'F' and resid 278 through 281 removed outlier: 6.223A pdb=" N VAL F 258 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU F 152 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLY F 260 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE F 210 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA F 261 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE F 212 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE F 176 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE F 211 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 150 through 152 removed outlier: 7.200A pdb=" N LYS A 278 " --> pdb=" O LEU A 151 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 174 through 178 removed outlier: 3.752A pdb=" N ILE B 209 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 257 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ILE B 212 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 259 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 278 through 282 removed outlier: 4.030A pdb=" N LYS C 278 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 150 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 258 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 152 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY C 260 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY C 154 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER C 208 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU C 259 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE C 210 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA C 261 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 212 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 278 through 281 removed outlier: 8.392A pdb=" N VAL D 150 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL D 258 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU D 152 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY D 260 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER D 208 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU D 259 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE D 210 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA D 261 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE D 212 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER D 174 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE D 211 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE D 176 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP D 213 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 278 through 281 removed outlier: 3.981A pdb=" N LYS E 278 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL E 258 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU E 152 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY E 260 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1044 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: 3.29 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4244 1.34 - 1.45: 1441 1.45 - 1.57: 7592 1.57 - 1.69: 25 1.69 - 1.81: 106 Bond restraints: 13408 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.03e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.55e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.55e+01 ... (remaining 13403 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.92: 543 106.92 - 114.27: 7899 114.27 - 121.61: 6759 121.61 - 128.96: 2890 128.96 - 136.30: 71 Bond angle restraints: 18162 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 117.03 22.84 1.00e+00 1.00e+00 5.22e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 118.44 21.43 1.00e+00 1.00e+00 4.59e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 119.06 20.81 1.00e+00 1.00e+00 4.33e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.14 19.73 1.00e+00 1.00e+00 3.89e+02 ... (remaining 18157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 7765 16.56 - 33.13: 437 33.13 - 49.69: 112 49.69 - 66.26: 21 66.26 - 82.82: 9 Dihedral angle restraints: 8344 sinusoidal: 3552 harmonic: 4792 Sorted by residual: dihedral pdb=" CA GLN B 206 " pdb=" C GLN B 206 " pdb=" N PRO B 207 " pdb=" CA PRO B 207 " ideal model delta harmonic sigma weight residual 180.00 134.48 45.52 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA GLN E 206 " pdb=" C GLN E 206 " pdb=" N PRO E 207 " pdb=" CA PRO E 207 " ideal model delta harmonic sigma weight residual 180.00 140.98 39.02 0 5.00e+00 4.00e-02 6.09e+01 dihedral pdb=" CA TYR B 129 " pdb=" C TYR B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 141.09 38.91 0 5.00e+00 4.00e-02 6.05e+01 ... (remaining 8341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1956 0.096 - 0.192: 98 0.192 - 0.288: 3 0.288 - 0.384: 2 0.384 - 0.480: 2 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CA ALA A 229 " pdb=" N ALA A 229 " pdb=" C ALA A 229 " pdb=" CB ALA A 229 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA GLU F 91 " pdb=" N GLU F 91 " pdb=" C GLU F 91 " pdb=" CB GLU F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA ILE A 215 " pdb=" N ILE A 215 " pdb=" C ILE A 215 " pdb=" CB ILE A 215 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2058 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 129 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO D 130 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 129 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO B 130 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 338 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLU B 338 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU B 338 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR B 339 " 0.020 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 59 2.36 - 3.00: 7429 3.00 - 3.63: 20718 3.63 - 4.27: 29818 4.27 - 4.90: 47849 Nonbonded interactions: 105873 Sorted by model distance: nonbonded pdb=" OD1 ASP A 213 " pdb=" OE1 GLN A 214 " model vdw 1.731 3.040 nonbonded pdb=" O2B ATP C 501 " pdb="MG MG C 502 " model vdw 1.997 2.170 nonbonded pdb=" O2B ATP A 501 " pdb="MG MG A 502 " model vdw 2.008 2.170 nonbonded pdb=" O2B ATP E 501 " pdb="MG MG E 502 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR C 161 " pdb="MG MG C 502 " model vdw 2.026 2.170 ... (remaining 105868 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 87 through 221 or resid 231 through 342)) selection = (chain 'B' and (resid 87 through 132 or resid 145 through 221 or resid 231 throu \ gh 243 or resid 252 through 342)) selection = (chain 'C' and (resid 87 through 132 or resid 145 through 221 or resid 231 throu \ gh 243 or resid 252 through 342)) selection = (chain 'D' and (resid 87 through 132 or resid 145 through 221 or resid 231 throu \ gh 243 or resid 252 through 342)) selection = (chain 'E' and (resid 87 through 132 or resid 145 through 221 or resid 231 throu \ gh 243 or resid 252 through 342)) selection = (chain 'F' and (resid 87 through 132 or resid 145 through 243 or resid 252 throu \ gh 342)) } 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: 0.870 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: 4.150 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 37.060 Find NCS groups from input model: 0.960 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 0.079 13408 Z= 0.285 Angle : 0.944 22.839 18162 Z= 0.687 Chirality : 0.049 0.480 2061 Planarity : 0.006 0.114 2340 Dihedral : 11.873 82.824 5250 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 42.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.34 % Favored : 88.54 % Rotamer: Outliers : 0.93 % Allowed : 5.65 % Favored : 93.42 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -3.81 (0.18), residues: 1632 helix: -1.98 (0.16), residues: 715 sheet: -2.31 (0.43), residues: 127 loop : -3.12 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP D 241 HIS 0.013 0.001 HIS A 179 PHE 0.018 0.002 PHE C 307 TYR 0.018 0.001 TYR D 129 ARG 0.009 0.001 ARG F 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 418 time to evaluate : 1.578 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: symmetry clash revert: symmetry clash REVERT: F 128 ILE cc_start: 0.8359 (pp) cc_final: 0.8141 (mt) REVERT: F 269 ASP cc_start: 0.7012 (t0) cc_final: 0.6783 (t0) REVERT: A 174 SER cc_start: 0.8378 (m) cc_final: 0.6177 (m) REVERT: B 55 GLU cc_start: 0.5997 (tm-30) cc_final: 0.5749 (tm-30) REVERT: B 263 ASN cc_start: 0.7664 (m110) cc_final: 0.7457 (m110) REVERT: B 342 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: C 105 ASP cc_start: 0.7548 (t0) cc_final: 0.7104 (t0) REVERT: C 148 SER cc_start: 0.8727 (t) cc_final: 0.8483 (m) REVERT: C 298 LEU cc_start: 0.8676 (mt) cc_final: 0.8419 (mt) outliers start: 13 outliers final: 7 residues processed: 429 average time/residue: 0.3188 time to fit residues: 183.2188 Evaluate side-chains 215 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 207 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 344 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 192 ASN A 94 ASN A 214 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 254 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN C 94 ASN C 169 HIS C 192 ASN C 214 GLN C 248 ASN D 56 ASN D 214 GLN D 248 ASN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 248 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13408 Z= 0.337 Angle : 0.810 11.921 18162 Z= 0.402 Chirality : 0.049 0.221 2061 Planarity : 0.007 0.115 2340 Dihedral : 11.317 87.499 2016 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.15 % Favored : 88.73 % Rotamer: Outliers : 4.29 % Allowed : 14.30 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -3.01 (0.19), residues: 1632 helix: -1.18 (0.19), residues: 712 sheet: -1.91 (0.41), residues: 130 loop : -2.82 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 241 HIS 0.005 0.001 HIS E 139 PHE 0.016 0.002 PHE F 199 TYR 0.014 0.002 TYR F 137 ARG 0.009 0.001 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 215 time to evaluate : 1.592 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7037 (t80) REVERT: F 268 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7380 (tp) REVERT: B 51 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7709 (tp) REVERT: B 94 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7733 (t0) REVERT: B 263 ASN cc_start: 0.7643 (m110) cc_final: 0.7426 (m-40) REVERT: B 342 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: B 344 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8215 (tmm160) REVERT: C 105 ASP cc_start: 0.7591 (t0) cc_final: 0.7172 (t0) REVERT: C 111 ASN cc_start: 0.7895 (t0) cc_final: 0.7592 (t0) REVERT: C 303 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6705 (pmt100) REVERT: E 133 MET cc_start: 0.8823 (ppp) cc_final: 0.8616 (ppp) outliers start: 60 outliers final: 37 residues processed: 253 average time/residue: 0.2824 time to fit residues: 103.2463 Evaluate side-chains 225 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN F 192 ASN A 214 GLN B 94 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 214 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13408 Z= 0.317 Angle : 0.748 11.031 18162 Z= 0.373 Chirality : 0.047 0.208 2061 Planarity : 0.006 0.112 2340 Dihedral : 10.907 86.470 2013 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.27 % Favored : 88.60 % Rotamer: Outliers : 6.36 % Allowed : 14.58 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -2.59 (0.20), residues: 1632 helix: -0.86 (0.19), residues: 723 sheet: -1.43 (0.44), residues: 126 loop : -2.64 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 241 HIS 0.004 0.001 HIS E 169 PHE 0.012 0.002 PHE A 280 TYR 0.014 0.002 TYR D 153 ARG 0.005 0.001 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 193 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7186 (t80) REVERT: F 268 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 62 ARG cc_start: 0.8071 (tpt170) cc_final: 0.7621 (tpt170) REVERT: A 316 THR cc_start: 0.7564 (p) cc_final: 0.7294 (p) REVERT: B 342 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: B 344 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8101 (tmm160) REVERT: C 105 ASP cc_start: 0.7558 (t0) cc_final: 0.7190 (t0) REVERT: C 111 ASN cc_start: 0.8032 (t0) cc_final: 0.7658 (t0) REVERT: C 303 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6699 (pmt100) REVERT: E 133 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7521 (ppp) outliers start: 89 outliers final: 52 residues processed: 255 average time/residue: 0.2503 time to fit residues: 92.4662 Evaluate side-chains 231 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 173 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 325 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.0970 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 263 ASN D 56 ASN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13408 Z= 0.210 Angle : 0.708 10.364 18162 Z= 0.351 Chirality : 0.045 0.216 2061 Planarity : 0.006 0.109 2340 Dihedral : 10.614 88.151 2013 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.66 % Favored : 89.28 % Rotamer: Outliers : 5.58 % Allowed : 17.37 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -2.26 (0.21), residues: 1632 helix: -0.54 (0.20), residues: 714 sheet: -1.20 (0.45), residues: 126 loop : -2.51 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 241 HIS 0.010 0.001 HIS C 227 PHE 0.016 0.002 PHE E 237 TYR 0.029 0.002 TYR D 153 ARG 0.005 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 191 time to evaluate : 1.557 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: F 92 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7158 (t80) REVERT: F 192 ASN cc_start: 0.8173 (m-40) cc_final: 0.7807 (m-40) REVERT: F 268 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7276 (tt) REVERT: A 62 ARG cc_start: 0.7887 (tpt170) cc_final: 0.7378 (tpt170) REVERT: A 184 THR cc_start: 0.9317 (p) cc_final: 0.9073 (p) REVERT: A 192 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7218 (p0) REVERT: A 316 THR cc_start: 0.7486 (p) cc_final: 0.7149 (p) REVERT: A 333 MET cc_start: 0.8577 (tpp) cc_final: 0.8324 (tpp) REVERT: B 205 LEU cc_start: 0.5575 (pt) cc_final: 0.5177 (pp) REVERT: B 344 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8109 (tmm160) REVERT: C 105 ASP cc_start: 0.7482 (t0) cc_final: 0.7138 (t0) REVERT: C 111 ASN cc_start: 0.8012 (t0) cc_final: 0.7631 (t0) REVERT: C 303 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6772 (pmt100) REVERT: E 133 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.7508 (ppp) outliers start: 78 outliers final: 45 residues processed: 246 average time/residue: 0.2383 time to fit residues: 86.1642 Evaluate side-chains 214 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 163 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 135 optimal weight: 0.1980 chunk 109 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13408 Z= 0.226 Angle : 0.699 10.158 18162 Z= 0.347 Chirality : 0.045 0.217 2061 Planarity : 0.006 0.107 2340 Dihedral : 10.401 87.450 2008 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.78 % Favored : 89.15 % Rotamer: Outliers : 5.43 % Allowed : 17.94 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -2.03 (0.21), residues: 1632 helix: -0.37 (0.20), residues: 706 sheet: -0.97 (0.47), residues: 126 loop : -2.36 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 241 HIS 0.007 0.001 HIS C 227 PHE 0.012 0.002 PHE C 175 TYR 0.021 0.002 TYR D 153 ARG 0.004 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 180 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 192 ASN cc_start: 0.8174 (m-40) cc_final: 0.7813 (m-40) REVERT: F 268 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7324 (tt) REVERT: A 62 ARG cc_start: 0.7764 (tpt170) cc_final: 0.7389 (tpt170) REVERT: A 92 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.6093 (t80) REVERT: A 184 THR cc_start: 0.9320 (p) cc_final: 0.9087 (p) REVERT: A 203 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.8010 (tppt) REVERT: A 316 THR cc_start: 0.7517 (p) cc_final: 0.7205 (p) REVERT: B 106 ILE cc_start: 0.8319 (mm) cc_final: 0.8079 (mm) REVERT: B 205 LEU cc_start: 0.5313 (pt) cc_final: 0.4784 (pp) REVERT: B 344 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8012 (tmm160) REVERT: C 105 ASP cc_start: 0.7519 (t0) cc_final: 0.7186 (t0) REVERT: C 111 ASN cc_start: 0.8042 (t0) cc_final: 0.7622 (t0) REVERT: C 303 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6747 (pmt100) REVERT: E 133 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.7538 (ppp) outliers start: 76 outliers final: 51 residues processed: 236 average time/residue: 0.2304 time to fit residues: 81.1010 Evaluate side-chains 226 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 169 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN F 94 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13408 Z= 0.246 Angle : 0.705 9.565 18162 Z= 0.350 Chirality : 0.045 0.198 2061 Planarity : 0.006 0.107 2340 Dihedral : 10.305 88.712 2004 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.91 % Favored : 88.97 % Rotamer: Outliers : 6.08 % Allowed : 18.08 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1632 helix: -0.32 (0.20), residues: 708 sheet: -0.80 (0.48), residues: 126 loop : -2.19 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 241 HIS 0.006 0.001 HIS C 227 PHE 0.012 0.002 PHE F 307 TYR 0.018 0.001 TYR D 153 ARG 0.004 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 179 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 192 ASN cc_start: 0.8204 (m-40) cc_final: 0.7839 (m-40) REVERT: F 268 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7331 (tt) REVERT: A 55 GLU cc_start: 0.5858 (tm-30) cc_final: 0.5543 (tm-30) REVERT: A 92 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6481 (t80) REVERT: A 184 THR cc_start: 0.9324 (p) cc_final: 0.9074 (p) REVERT: A 192 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7410 (p0) REVERT: A 203 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8064 (tppt) REVERT: B 344 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8061 (tmm160) REVERT: C 105 ASP cc_start: 0.7541 (t0) cc_final: 0.7207 (t0) REVERT: C 111 ASN cc_start: 0.8119 (t0) cc_final: 0.7708 (t0) REVERT: C 303 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6762 (pmt100) REVERT: D 153 TYR cc_start: 0.8217 (p90) cc_final: 0.7989 (p90) REVERT: D 163 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8559 (mt) REVERT: E 133 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.7551 (ppp) outliers start: 85 outliers final: 56 residues processed: 240 average time/residue: 0.2334 time to fit residues: 82.8887 Evaluate side-chains 234 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 170 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 0.0060 chunk 89 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN F 192 ASN C 179 HIS C 227 HIS ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13408 Z= 0.264 Angle : 0.714 10.857 18162 Z= 0.356 Chirality : 0.046 0.207 2061 Planarity : 0.006 0.107 2340 Dihedral : 10.367 88.974 2004 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.72 % Favored : 89.22 % Rotamer: Outliers : 6.36 % Allowed : 18.37 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.21), residues: 1632 helix: -0.30 (0.20), residues: 722 sheet: -0.62 (0.50), residues: 118 loop : -2.19 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 241 HIS 0.010 0.001 HIS C 227 PHE 0.015 0.002 PHE C 175 TYR 0.016 0.001 TYR D 153 ARG 0.004 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 180 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 192 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7842 (m-40) REVERT: F 268 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7344 (tt) REVERT: A 62 ARG cc_start: 0.7999 (tpt170) cc_final: 0.7646 (tpt170) REVERT: A 92 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.6327 (t80) REVERT: A 184 THR cc_start: 0.9348 (p) cc_final: 0.9098 (p) REVERT: A 192 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7473 (p0) REVERT: A 316 THR cc_start: 0.7533 (p) cc_final: 0.7315 (p) REVERT: C 105 ASP cc_start: 0.7599 (t0) cc_final: 0.7250 (t0) REVERT: C 111 ASN cc_start: 0.8160 (t0) cc_final: 0.7752 (t0) REVERT: C 303 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6491 (pmt100) REVERT: D 163 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8595 (mt) REVERT: E 133 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.7591 (ppp) outliers start: 89 outliers final: 59 residues processed: 242 average time/residue: 0.2287 time to fit residues: 82.4295 Evaluate side-chains 233 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 167 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 325 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN A 254 ASN C 179 HIS ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13408 Z= 0.214 Angle : 0.715 11.718 18162 Z= 0.353 Chirality : 0.045 0.176 2061 Planarity : 0.006 0.106 2340 Dihedral : 10.166 89.553 2000 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.66 % Favored : 89.28 % Rotamer: Outliers : 5.58 % Allowed : 19.44 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.68 (0.21), residues: 1632 helix: -0.16 (0.20), residues: 710 sheet: -0.61 (0.49), residues: 118 loop : -2.12 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 241 HIS 0.003 0.001 HIS B 227 PHE 0.013 0.001 PHE C 175 TYR 0.029 0.001 TYR D 153 ARG 0.004 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 179 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 268 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7240 (tt) REVERT: A 92 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.6239 (t80) REVERT: A 184 THR cc_start: 0.9353 (p) cc_final: 0.9102 (p) REVERT: A 192 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7430 (p0) REVERT: C 105 ASP cc_start: 0.7564 (t0) cc_final: 0.7234 (t0) REVERT: C 111 ASN cc_start: 0.8185 (t0) cc_final: 0.7777 (t0) REVERT: C 303 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6481 (pmt100) REVERT: D 163 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8500 (mt) REVERT: E 133 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7556 (ppp) outliers start: 78 outliers final: 57 residues processed: 233 average time/residue: 0.2428 time to fit residues: 85.9518 Evaluate side-chains 232 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 169 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.4980 chunk 151 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 146 optimal weight: 0.0000 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 192 ASN F 254 ASN C 179 HIS ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13408 Z= 0.188 Angle : 0.713 13.023 18162 Z= 0.349 Chirality : 0.045 0.268 2061 Planarity : 0.006 0.106 2340 Dihedral : 9.977 86.461 2000 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.57 % Allowed : 20.30 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.54 (0.22), residues: 1632 helix: -0.03 (0.20), residues: 702 sheet: -0.61 (0.48), residues: 121 loop : -2.03 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 187 HIS 0.011 0.001 HIS C 179 PHE 0.012 0.001 PHE A 280 TYR 0.027 0.001 TYR D 153 ARG 0.009 0.000 ARG F 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 181 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 192 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7793 (m-40) REVERT: F 268 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7119 (tp) REVERT: A 62 ARG cc_start: 0.7844 (tpt170) cc_final: 0.7623 (tpt170) REVERT: A 92 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.6100 (t80) REVERT: A 184 THR cc_start: 0.9355 (p) cc_final: 0.9105 (p) REVERT: A 192 ASN cc_start: 0.7683 (p0) cc_final: 0.7456 (p0) REVERT: C 105 ASP cc_start: 0.7588 (t0) cc_final: 0.7270 (t0) REVERT: C 111 ASN cc_start: 0.8158 (t0) cc_final: 0.7770 (t0) REVERT: C 303 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6763 (pmt100) REVERT: D 163 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8512 (mt) REVERT: E 133 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7628 (ppp) outliers start: 64 outliers final: 51 residues processed: 225 average time/residue: 0.2218 time to fit residues: 75.2202 Evaluate side-chains 227 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 170 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 100 optimal weight: 0.0010 chunk 79 optimal weight: 4.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13408 Z= 0.250 Angle : 0.739 13.894 18162 Z= 0.366 Chirality : 0.046 0.312 2061 Planarity : 0.006 0.106 2340 Dihedral : 9.981 86.671 2000 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 4.29 % Allowed : 20.87 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.54 (0.22), residues: 1632 helix: -0.06 (0.20), residues: 704 sheet: -0.55 (0.48), residues: 121 loop : -2.02 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 187 HIS 0.003 0.001 HIS B 227 PHE 0.011 0.002 PHE F 307 TYR 0.026 0.001 TYR D 153 ARG 0.006 0.000 ARG B 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 167 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 192 ASN cc_start: 0.8194 (m-40) cc_final: 0.7987 (m110) REVERT: F 268 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7214 (tt) REVERT: A 62 ARG cc_start: 0.7832 (tpt170) cc_final: 0.7604 (tpt170) REVERT: A 92 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.6168 (t80) REVERT: A 184 THR cc_start: 0.9360 (p) cc_final: 0.9111 (p) REVERT: A 192 ASN cc_start: 0.7710 (p0) cc_final: 0.7479 (p0) REVERT: C 105 ASP cc_start: 0.7611 (t0) cc_final: 0.7288 (t0) REVERT: C 111 ASN cc_start: 0.8178 (t0) cc_final: 0.7799 (t0) REVERT: C 303 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6840 (pmt100) REVERT: D 163 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8532 (mt) REVERT: E 133 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7644 (ppp) outliers start: 60 outliers final: 52 residues processed: 208 average time/residue: 0.2276 time to fit residues: 70.7532 Evaluate side-chains 224 residues out of total 1399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 167 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 36 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 chunk 133 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 192 ASN C 95 GLN ** E 94 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.128195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103655 restraints weight = 26802.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103545 restraints weight = 18259.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104201 restraints weight = 15484.763| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13408 Z= 0.189 Angle : 0.715 14.187 18162 Z= 0.353 Chirality : 0.045 0.292 2061 Planarity : 0.005 0.103 2340 Dihedral : 9.580 84.326 1997 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 4.22 % Allowed : 21.02 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.42 (0.22), residues: 1632 helix: 0.11 (0.21), residues: 694 sheet: -0.46 (0.48), residues: 121 loop : -2.01 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 187 HIS 0.003 0.001 HIS D 343 PHE 0.012 0.001 PHE A 280 TYR 0.026 0.001 TYR D 153 ARG 0.003 0.000 ARG C 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.23 seconds wall clock time: 50 minutes 17.13 seconds (3017.13 seconds total)