Starting phenix.real_space_refine on Fri Mar 15 19:06:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/03_2024/6ndy_0443_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/03_2024/6ndy_0443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/03_2024/6ndy_0443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/03_2024/6ndy_0443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/03_2024/6ndy_0443_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/03_2024/6ndy_0443_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.006 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 45 5.16 5 Be 3 3.05 5 C 7846 2.51 5 N 2143 2.21 5 O 2471 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 247": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12531 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2427 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "E" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2360 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 120 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 19} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.76, per 1000 atoms: 0.54 Number of scatterers: 12531 At special positions: 0 Unit cell: (79.57, 141.7, 156.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 10 15.00 Mg 4 11.99 F 9 9.00 O 2471 8.00 N 2143 7.00 C 7846 6.00 Be 3 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 11 sheets defined 42.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.739A pdb=" N SER A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 121 " --> pdb=" O ALA A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 121' Processing helix chain 'A' and resid 139 through 154 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 209 through 223 removed outlier: 4.004A pdb=" N VAL A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 246 through 259 removed outlier: 4.709A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 336 through 355 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 419 through 432 Processing helix chain 'B' and resid 113 through 122 removed outlier: 4.440A pdb=" N SER B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 179 through 189 Processing helix chain 'B' and resid 209 through 223 removed outlier: 4.313A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 336 through 355 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 139 through 154 Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 210 through 223 removed outlier: 3.588A pdb=" N VAL C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'C' and resid 336 through 355 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'D' and resid 113 through 122 removed outlier: 4.658A pdb=" N SER D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 139 through 154 Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 199 through 202 No H-bonds generated for 'chain 'D' and resid 199 through 202' Processing helix chain 'D' and resid 210 through 223 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 336 through 355 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'E' and resid 139 through 154 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 179 through 189 Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 234 through 237 No H-bonds generated for 'chain 'E' and resid 234 through 237' Processing helix chain 'E' and resid 246 through 260 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'E' and resid 336 through 355 Proline residue: E 350 - end of helix removed outlier: 3.557A pdb=" N GLN E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 420 through 431 Processing sheet with id= A, first strand: chain 'A' and resid 169 through 173 removed outlier: 6.542A pdb=" N ARG A 292 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N TYR A 172 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 294 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 193 through 197 Processing sheet with id= C, first strand: chain 'A' and resid 360 through 363 removed outlier: 4.037A pdb=" N LYS A 372 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 293 through 296 removed outlier: 6.213A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE B 296 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR B 172 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 173 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 360 through 362 Processing sheet with id= F, first strand: chain 'C' and resid 292 through 296 removed outlier: 3.639A pdb=" N ARG C 292 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE C 169 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 272 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU C 171 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY C 274 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY C 173 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 276 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER C 227 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU C 273 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA C 275 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE C 231 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 193 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE C 230 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE C 195 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP C 232 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 197 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 360 through 362 Processing sheet with id= H, first strand: chain 'D' and resid 292 through 296 removed outlier: 3.569A pdb=" N GLY D 173 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N SER D 227 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE D 195 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP D 232 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 197 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 360 through 363 removed outlier: 3.597A pdb=" N VAL D 363 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS D 372 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 292 through 296 removed outlier: 6.663A pdb=" N SER E 227 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 273 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE E 229 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA E 275 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 231 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR E 193 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE E 230 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE E 195 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 232 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 360 through 363 removed outlier: 4.255A pdb=" N LYS E 372 " --> pdb=" O VAL E 363 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1317 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: 3.10 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4106 1.34 - 1.46: 2151 1.46 - 1.58: 6385 1.58 - 1.69: 15 1.69 - 1.81: 80 Bond restraints: 12737 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C5 ADP A 501 " pdb=" C6 ADP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 12732 not shown) Histogram of bond angle deviations from ideal: 99.95 - 107.16: 446 107.16 - 114.36: 7570 114.36 - 121.57: 6182 121.57 - 128.78: 2946 128.78 - 135.99: 79 Bond angle restraints: 17223 Sorted by residual: angle pdb=" C ASN E 265 " pdb=" N ASP E 266 " pdb=" CA ASP E 266 " ideal model delta sigma weight residual 122.46 130.35 -7.89 1.41e+00 5.03e-01 3.13e+01 angle pdb=" C GLY B 239 " pdb=" N THR B 240 " pdb=" CA THR B 240 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 angle pdb=" O1B ADP A 501 " pdb=" PB ADP A 501 " pdb=" O3B ADP A 501 " ideal model delta sigma weight residual 119.90 104.96 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O2B ADP B 501 " pdb=" PB ADP B 501 " pdb=" O3B ADP B 501 " ideal model delta sigma weight residual 119.90 104.96 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O2B ADP C 501 " pdb=" PB ADP C 501 " pdb=" O3B ADP C 501 " ideal model delta sigma weight residual 119.90 105.52 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 17218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.41: 7581 32.41 - 64.82: 196 64.82 - 97.23: 14 97.23 - 129.63: 3 129.63 - 162.04: 2 Dihedral angle restraints: 7796 sinusoidal: 3213 harmonic: 4583 Sorted by residual: dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 102.04 -162.04 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 73.34 -133.34 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 178.17 121.83 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 7793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1612 0.056 - 0.113: 272 0.113 - 0.169: 62 0.169 - 0.225: 9 0.225 - 0.282: 2 Chirality restraints: 1957 Sorted by residual: chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 278 " pdb=" CA ILE C 278 " pdb=" CG1 ILE C 278 " pdb=" CG2 ILE C 278 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE A 228 " pdb=" CA ILE A 228 " pdb=" CG1 ILE A 228 " pdb=" CG2 ILE A 228 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1954 not shown) Planarity restraints: 2206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 147 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C GLU C 147 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU C 147 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 148 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 349 " -0.038 5.00e-02 4.00e+02 5.60e-02 5.03e+00 pdb=" N PRO C 350 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 350 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 350 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 374 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 375 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 375 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 375 " 0.030 5.00e-02 4.00e+02 ... (remaining 2203 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 167 2.61 - 3.18: 10034 3.18 - 3.75: 19484 3.75 - 4.33: 25510 4.33 - 4.90: 43043 Nonbonded interactions: 98238 Sorted by model distance: nonbonded pdb=" OG SER A 180 " pdb="MG MG A 503 " model vdw 2.037 2.170 nonbonded pdb=" OG SER C 180 " pdb="MG MG C 503 " model vdw 2.038 2.170 nonbonded pdb=" F1 BEF C 502 " pdb="MG MG C 503 " model vdw 2.038 2.120 nonbonded pdb=" OG SER B 180 " pdb="MG MG B 503 " model vdw 2.038 2.170 nonbonded pdb=" O2B ADP A 501 " pdb="MG MG A 503 " model vdw 2.038 2.170 ... (remaining 98233 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 126 through 433) selection = (chain 'B' and resid 126 through 433) selection = (chain 'C' and resid 126 through 433) selection = (chain 'D' and resid 126 through 433) selection = (chain 'E' and resid 126 through 433) } 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: 0.900 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: 3.990 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 33.360 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 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 : 0.005 0.104 12737 Z= 0.300 Angle : 0.892 14.941 17223 Z= 0.451 Chirality : 0.048 0.282 1957 Planarity : 0.006 0.056 2206 Dihedral : 14.707 162.042 4830 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.16), residues: 1574 helix: -2.38 (0.12), residues: 751 sheet: -2.34 (0.39), residues: 160 loop : -2.54 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 280 HIS 0.001 0.000 HIS A 359 PHE 0.011 0.001 PHE A 308 TYR 0.008 0.001 TYR C 181 ARG 0.002 0.000 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.6605 (mt0) cc_final: 0.6379 (tt0) REVERT: A 343 VAL cc_start: 0.7244 (t) cc_final: 0.6741 (t) REVERT: A 351 ILE cc_start: 0.6725 (mp) cc_final: 0.6227 (mm) REVERT: B 162 ASN cc_start: 0.6193 (m110) cc_final: 0.5772 (t0) REVERT: C 289 ARG cc_start: 0.4564 (mmt90) cc_final: 0.3295 (mmt90) REVERT: C 373 LEU cc_start: 0.7974 (mp) cc_final: 0.7663 (tp) REVERT: D 355 GLN cc_start: 0.6696 (mt0) cc_final: 0.6204 (tt0) REVERT: D 425 GLN cc_start: 0.5833 (mm-40) cc_final: 0.5472 (mt0) REVERT: E 157 HIS cc_start: 0.5602 (p90) cc_final: 0.5375 (p-80) REVERT: E 233 GLU cc_start: 0.7046 (mp0) cc_final: 0.6580 (mp0) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2837 time to fit residues: 163.3982 Evaluate side-chains 207 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 355 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 311 ASN B 427 GLN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN D 216 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12737 Z= 0.211 Angle : 0.713 11.950 17223 Z= 0.342 Chirality : 0.042 0.235 1957 Planarity : 0.005 0.048 2206 Dihedral : 8.848 156.046 1756 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.74 % Allowed : 15.31 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.19), residues: 1574 helix: -0.62 (0.17), residues: 766 sheet: -1.57 (0.41), residues: 162 loop : -2.13 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 206 HIS 0.003 0.001 HIS D 157 PHE 0.013 0.002 PHE B 406 TYR 0.023 0.002 TYR C 181 ARG 0.007 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 239 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.6831 (mt) cc_final: 0.6227 (mt) REVERT: A 216 GLN cc_start: 0.6937 (mt0) cc_final: 0.6732 (tt0) REVERT: A 306 THR cc_start: 0.8071 (m) cc_final: 0.7819 (p) REVERT: A 348 MET cc_start: 0.7757 (tpp) cc_final: 0.7001 (tpp) REVERT: B 307 MET cc_start: 0.6323 (mtp) cc_final: 0.6062 (mtp) REVERT: C 113 LYS cc_start: 0.6272 (pttm) cc_final: 0.5921 (mtmm) REVERT: D 360 PHE cc_start: 0.4246 (m-10) cc_final: 0.3868 (m-80) REVERT: D 425 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6355 (mt0) REVERT: E 425 GLN cc_start: 0.6246 (mm110) cc_final: 0.5975 (mm-40) outliers start: 37 outliers final: 21 residues processed: 260 average time/residue: 0.2151 time to fit residues: 83.9949 Evaluate side-chains 196 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.0470 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12737 Z= 0.211 Angle : 0.664 7.612 17223 Z= 0.318 Chirality : 0.043 0.286 1957 Planarity : 0.005 0.045 2206 Dihedral : 8.053 136.335 1756 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.25 % Allowed : 17.75 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.21), residues: 1574 helix: 0.05 (0.18), residues: 763 sheet: -1.28 (0.42), residues: 165 loop : -1.75 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 280 HIS 0.003 0.001 HIS A 157 PHE 0.018 0.002 PHE D 195 TYR 0.025 0.002 TYR D 324 ARG 0.007 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.7232 (mt0) cc_final: 0.6968 (tt0) REVERT: A 306 THR cc_start: 0.8105 (m) cc_final: 0.7898 (p) REVERT: A 348 MET cc_start: 0.7969 (tpp) cc_final: 0.7276 (tpp) REVERT: B 123 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5714 (tp) REVERT: B 386 MET cc_start: 0.3694 (ptt) cc_final: 0.3442 (ptt) REVERT: B 432 PHE cc_start: 0.7729 (m-10) cc_final: 0.7482 (m-10) REVERT: C 113 LYS cc_start: 0.6247 (pttm) cc_final: 0.5862 (mtmm) REVERT: D 129 ASN cc_start: 0.7407 (m-40) cc_final: 0.7134 (m-40) REVERT: D 310 ILE cc_start: 0.7031 (pt) cc_final: 0.6782 (mt) REVERT: D 360 PHE cc_start: 0.4838 (m-10) cc_final: 0.4520 (m-80) REVERT: D 421 ASP cc_start: 0.8030 (t0) cc_final: 0.7744 (t0) REVERT: D 425 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6849 (mm-40) REVERT: E 388 TRP cc_start: 0.6912 (p90) cc_final: 0.6389 (p-90) outliers start: 44 outliers final: 26 residues processed: 224 average time/residue: 0.1935 time to fit residues: 66.6324 Evaluate side-chains 184 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.0060 chunk 107 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12737 Z= 0.191 Angle : 0.639 8.146 17223 Z= 0.300 Chirality : 0.043 0.259 1957 Planarity : 0.004 0.042 2206 Dihedral : 7.715 136.497 1756 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.11 % Allowed : 19.30 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1574 helix: 0.49 (0.19), residues: 739 sheet: -1.23 (0.42), residues: 160 loop : -1.46 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 280 HIS 0.003 0.001 HIS D 359 PHE 0.023 0.001 PHE D 428 TYR 0.022 0.002 TYR A 172 ARG 0.004 0.000 ARG E 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.7373 (mt0) cc_final: 0.7081 (tt0) REVERT: A 306 THR cc_start: 0.8264 (m) cc_final: 0.8048 (p) REVERT: A 348 MET cc_start: 0.7903 (tpp) cc_final: 0.7087 (tpp) REVERT: B 268 GLN cc_start: 0.6847 (tm-30) cc_final: 0.6567 (pm20) REVERT: B 330 MET cc_start: 0.9039 (mmp) cc_final: 0.8835 (mmp) REVERT: B 360 PHE cc_start: 0.6355 (m-80) cc_final: 0.6011 (m-80) REVERT: B 386 MET cc_start: 0.4170 (ptt) cc_final: 0.3565 (ptt) REVERT: B 432 PHE cc_start: 0.7959 (m-80) cc_final: 0.7718 (m-10) REVERT: C 113 LYS cc_start: 0.5926 (pttm) cc_final: 0.5557 (mtmm) REVERT: C 260 MET cc_start: 0.7568 (ttm) cc_final: 0.7233 (ttp) REVERT: D 169 ILE cc_start: 0.7766 (mm) cc_final: 0.7531 (mm) REVERT: D 310 ILE cc_start: 0.7332 (pt) cc_final: 0.7095 (mt) REVERT: D 360 PHE cc_start: 0.4817 (m-10) cc_final: 0.4527 (m-80) REVERT: D 421 ASP cc_start: 0.8059 (t0) cc_final: 0.7853 (t70) REVERT: D 425 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7289 (mm-40) REVERT: E 388 TRP cc_start: 0.6849 (p90) cc_final: 0.6381 (p-90) outliers start: 42 outliers final: 24 residues processed: 200 average time/residue: 0.1700 time to fit residues: 52.2977 Evaluate side-chains 173 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 129 optimal weight: 0.0980 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 311 ASN D 162 ASN D 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12737 Z= 0.184 Angle : 0.636 12.350 17223 Z= 0.295 Chirality : 0.043 0.287 1957 Planarity : 0.004 0.039 2206 Dihedral : 7.337 126.881 1756 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.33 % Allowed : 19.82 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1574 helix: 0.75 (0.19), residues: 736 sheet: -0.99 (0.43), residues: 159 loop : -1.22 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 280 HIS 0.006 0.001 HIS C 359 PHE 0.017 0.001 PHE D 428 TYR 0.018 0.001 TYR A 172 ARG 0.004 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 157 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 MET cc_start: 0.7939 (tpp) cc_final: 0.7386 (tpp) REVERT: B 319 LEU cc_start: 0.7869 (mm) cc_final: 0.7566 (mm) REVERT: B 360 PHE cc_start: 0.6217 (m-80) cc_final: 0.5977 (m-80) REVERT: B 386 MET cc_start: 0.4365 (ptt) cc_final: 0.3857 (ptt) REVERT: C 113 LYS cc_start: 0.5864 (pttm) cc_final: 0.5507 (mtmm) REVERT: D 169 ILE cc_start: 0.8295 (mm) cc_final: 0.8017 (mm) REVERT: D 360 PHE cc_start: 0.5010 (m-10) cc_final: 0.4650 (m-80) REVERT: E 149 VAL cc_start: 0.7267 (t) cc_final: 0.7011 (t) REVERT: E 348 MET cc_start: 0.6528 (mmt) cc_final: 0.5907 (ppp) REVERT: E 388 TRP cc_start: 0.6784 (p90) cc_final: 0.6321 (p-90) outliers start: 45 outliers final: 29 residues processed: 191 average time/residue: 0.1995 time to fit residues: 58.3072 Evaluate side-chains 165 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.8473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12737 Z= 0.176 Angle : 0.622 8.844 17223 Z= 0.293 Chirality : 0.042 0.317 1957 Planarity : 0.004 0.036 2206 Dihedral : 7.300 127.641 1756 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.51 % Allowed : 20.71 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.22), residues: 1574 helix: 0.89 (0.20), residues: 732 sheet: -1.22 (0.42), residues: 171 loop : -1.07 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.004 0.001 HIS D 359 PHE 0.020 0.001 PHE C 360 TYR 0.016 0.001 TYR A 172 ARG 0.004 0.000 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 LEU cc_start: 0.8052 (mm) cc_final: 0.7823 (mm) REVERT: B 348 MET cc_start: 0.8342 (tpt) cc_final: 0.8106 (tpt) REVERT: B 360 PHE cc_start: 0.6473 (m-80) cc_final: 0.6175 (m-80) REVERT: B 386 MET cc_start: 0.4310 (ptt) cc_final: 0.3705 (ptt) REVERT: B 401 LEU cc_start: 0.9238 (mp) cc_final: 0.9008 (mp) REVERT: C 113 LYS cc_start: 0.5783 (pttm) cc_final: 0.5419 (mtmm) REVERT: C 260 MET cc_start: 0.7509 (ttm) cc_final: 0.7168 (mtp) REVERT: C 432 PHE cc_start: 0.8504 (m-80) cc_final: 0.8116 (m-80) REVERT: D 169 ILE cc_start: 0.8430 (mm) cc_final: 0.8207 (mm) REVERT: D 360 PHE cc_start: 0.4921 (m-10) cc_final: 0.4481 (m-80) REVERT: E 348 MET cc_start: 0.6566 (mmt) cc_final: 0.5881 (ppp) REVERT: E 388 TRP cc_start: 0.6753 (p90) cc_final: 0.6279 (p-90) outliers start: 34 outliers final: 23 residues processed: 170 average time/residue: 0.2017 time to fit residues: 52.9788 Evaluate side-chains 150 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.9413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12737 Z= 0.176 Angle : 0.626 10.072 17223 Z= 0.296 Chirality : 0.042 0.329 1957 Planarity : 0.004 0.037 2206 Dihedral : 7.123 123.425 1756 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.59 % Allowed : 21.30 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1574 helix: 0.90 (0.19), residues: 739 sheet: -1.16 (0.41), residues: 171 loop : -0.94 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 280 HIS 0.004 0.001 HIS D 359 PHE 0.018 0.001 PHE C 360 TYR 0.014 0.001 TYR A 172 ARG 0.003 0.000 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7770 (mtt) cc_final: 0.7025 (mtm) REVERT: A 220 MET cc_start: 0.6789 (ptm) cc_final: 0.6589 (ptm) REVERT: A 351 ILE cc_start: 0.8209 (mp) cc_final: 0.7872 (mm) REVERT: B 360 PHE cc_start: 0.6462 (m-80) cc_final: 0.6107 (m-80) REVERT: B 386 MET cc_start: 0.4677 (ptt) cc_final: 0.4271 (ptt) REVERT: C 113 LYS cc_start: 0.5738 (pttm) cc_final: 0.5388 (mtmm) REVERT: D 169 ILE cc_start: 0.8719 (mm) cc_final: 0.8430 (mt) REVERT: D 360 PHE cc_start: 0.5203 (m-10) cc_final: 0.4805 (m-80) REVERT: E 149 VAL cc_start: 0.7443 (t) cc_final: 0.7162 (t) REVERT: E 348 MET cc_start: 0.6497 (mmt) cc_final: 0.5859 (ppp) REVERT: E 388 TRP cc_start: 0.6697 (p90) cc_final: 0.6189 (p-90) outliers start: 35 outliers final: 20 residues processed: 163 average time/residue: 0.2246 time to fit residues: 54.9483 Evaluate side-chains 139 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain E residue 145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 0.0670 chunk 103 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 281 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 1.0320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12737 Z= 0.220 Angle : 0.674 9.775 17223 Z= 0.318 Chirality : 0.044 0.360 1957 Planarity : 0.005 0.080 2206 Dihedral : 7.336 126.052 1756 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.37 % Allowed : 22.34 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1574 helix: 0.74 (0.19), residues: 743 sheet: -1.15 (0.41), residues: 170 loop : -0.86 (0.26), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 388 HIS 0.004 0.001 HIS D 359 PHE 0.016 0.001 PHE D 428 TYR 0.015 0.002 TYR A 172 ARG 0.009 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.7440 (mtt) cc_final: 0.6911 (mtm) REVERT: B 360 PHE cc_start: 0.6309 (m-80) cc_final: 0.6082 (m-80) REVERT: B 386 MET cc_start: 0.5099 (ptt) cc_final: 0.4742 (ptt) REVERT: C 113 LYS cc_start: 0.6001 (pttm) cc_final: 0.5652 (mtmm) REVERT: C 432 PHE cc_start: 0.8717 (m-80) cc_final: 0.8416 (m-80) REVERT: D 235 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7551 (p0) REVERT: D 360 PHE cc_start: 0.5308 (m-10) cc_final: 0.4758 (m-80) REVERT: E 388 TRP cc_start: 0.6554 (p90) cc_final: 0.6009 (p-90) outliers start: 32 outliers final: 21 residues processed: 158 average time/residue: 0.2166 time to fit residues: 52.2919 Evaluate side-chains 137 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 429 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 1.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12737 Z= 0.247 Angle : 0.661 8.610 17223 Z= 0.314 Chirality : 0.044 0.355 1957 Planarity : 0.004 0.044 2206 Dihedral : 7.407 126.310 1756 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.14 % Allowed : 22.78 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1574 helix: 0.73 (0.19), residues: 731 sheet: -1.08 (0.41), residues: 167 loop : -0.92 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 280 HIS 0.004 0.001 HIS D 359 PHE 0.019 0.002 PHE C 360 TYR 0.013 0.002 TYR A 172 ARG 0.004 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: B 220 MET cc_start: 0.8148 (ptm) cc_final: 0.7882 (ptm) REVERT: B 347 LEU cc_start: 0.8838 (mt) cc_final: 0.8638 (mp) REVERT: B 360 PHE cc_start: 0.6639 (m-80) cc_final: 0.6133 (m-80) REVERT: B 386 MET cc_start: 0.5578 (ptt) cc_final: 0.5133 (ptt) REVERT: C 113 LYS cc_start: 0.5925 (pttm) cc_final: 0.5539 (mtmm) REVERT: D 123 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8520 (mt) REVERT: D 360 PHE cc_start: 0.5514 (m-10) cc_final: 0.4908 (m-80) REVERT: E 149 VAL cc_start: 0.8157 (t) cc_final: 0.7835 (t) REVERT: E 388 TRP cc_start: 0.6570 (p90) cc_final: 0.6016 (p-90) outliers start: 29 outliers final: 23 residues processed: 135 average time/residue: 0.2080 time to fit residues: 43.7426 Evaluate side-chains 125 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 1.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12737 Z= 0.179 Angle : 0.655 12.231 17223 Z= 0.306 Chirality : 0.043 0.370 1957 Planarity : 0.004 0.045 2206 Dihedral : 7.162 121.998 1756 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.63 % Allowed : 23.45 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1574 helix: 0.82 (0.19), residues: 737 sheet: -0.84 (0.42), residues: 164 loop : -0.86 (0.26), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 280 HIS 0.004 0.001 HIS D 359 PHE 0.015 0.001 PHE D 428 TYR 0.013 0.001 TYR A 172 ARG 0.006 0.000 ARG D 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: B 347 LEU cc_start: 0.8831 (mt) cc_final: 0.8612 (mp) REVERT: B 360 PHE cc_start: 0.6584 (m-80) cc_final: 0.6143 (m-80) REVERT: B 386 MET cc_start: 0.5369 (ptt) cc_final: 0.5030 (ptt) REVERT: C 113 LYS cc_start: 0.5920 (pttm) cc_final: 0.5579 (mtmm) REVERT: D 123 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8478 (mt) REVERT: D 360 PHE cc_start: 0.5651 (m-10) cc_final: 0.5040 (m-80) REVERT: E 149 VAL cc_start: 0.8212 (t) cc_final: 0.7872 (t) REVERT: E 388 TRP cc_start: 0.6558 (p90) cc_final: 0.6070 (p-90) outliers start: 22 outliers final: 14 residues processed: 123 average time/residue: 0.1953 time to fit residues: 38.0993 Evaluate side-chains 119 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 432 PHE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 GLN D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083923 restraints weight = 29378.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083124 restraints weight = 21611.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083618 restraints weight = 18182.982| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 1.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12737 Z= 0.172 Angle : 0.637 11.130 17223 Z= 0.300 Chirality : 0.043 0.371 1957 Planarity : 0.004 0.047 2206 Dihedral : 6.980 117.834 1756 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.63 % Allowed : 23.45 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1574 helix: 0.70 (0.19), residues: 756 sheet: -0.70 (0.42), residues: 164 loop : -0.86 (0.27), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 280 HIS 0.004 0.001 HIS D 359 PHE 0.017 0.001 PHE C 360 TYR 0.012 0.001 TYR A 172 ARG 0.003 0.000 ARG D 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2340.23 seconds wall clock time: 44 minutes 56.75 seconds (2696.75 seconds total)