Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 19:38:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2023/6ndy_0443_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2023/6ndy_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_0443/08_2023/6ndy_0443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2023/6ndy_0443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2023/6ndy_0443_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2023/6ndy_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-1.21rc1-5044/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: 6.45, per 1000 atoms: 0.51 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: 4.89 Conformation dependent library (CDL) restraints added in 2.0 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: 1.82 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: 3.31 Time building geometry restraints manager: 5.17 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: 0.980 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: 4.470 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.280 Find NCS groups from input model: 0.850 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2866 time to fit residues: 164.8315 Evaluate side-chains 202 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7883 ------------------------------------------------------------------------------- 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: 0.9980 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: 6.9990 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 162 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 311 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.3904 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= 0.217 Angle : 0.704 12.150 17223 Z= 0.337 Chirality : 0.043 0.211 1957 Planarity : 0.005 0.042 2206 Dihedral : 8.957 157.102 1756 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 2.66 % 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: -2.03 (0.20), residues: 1574 helix: -0.56 (0.17), residues: 766 sheet: -1.66 (0.40), residues: 165 loop : -2.15 (0.22), residues: 643 *********************** 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 281 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 264 average time/residue: 0.2172 time to fit residues: 85.0472 Evaluate side-chains 201 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1143 time to fit residues: 6.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 142 optimal weight: 0.0570 chunk 154 optimal weight: 6.9990 chunk 127 optimal weight: 0.0470 chunk 141 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN C 277 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 12737 Z= 0.225 Angle : 0.704 8.145 17223 Z= 0.339 Chirality : 0.044 0.181 1957 Planarity : 0.005 0.050 2206 Dihedral : 8.066 132.695 1756 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 2.81 % 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: -1.32 (0.21), residues: 1574 helix: -0.08 (0.18), residues: 763 sheet: -1.18 (0.44), residues: 153 loop : -1.69 (0.24), residues: 658 *********************** 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 230 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 219 average time/residue: 0.2095 time to fit residues: 69.3234 Evaluate side-chains 165 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1116 time to fit residues: 5.4680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 68 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 355 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 311 ASN D 425 GLN D 434 GLN E 355 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12737 Z= 0.187 Angle : 0.653 11.486 17223 Z= 0.308 Chirality : 0.043 0.287 1957 Planarity : 0.004 0.046 2206 Dihedral : 7.670 132.409 1756 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 1.55 % 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: -0.81 (0.22), residues: 1574 helix: 0.40 (0.19), residues: 738 sheet: -1.08 (0.43), residues: 161 loop : -1.41 (0.25), residues: 675 *********************** 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 181 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 172 average time/residue: 0.2069 time to fit residues: 54.6500 Evaluate side-chains 142 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1179 time to fit residues: 3.2076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.7967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 12737 Z= 0.172 Angle : 0.621 10.102 17223 Z= 0.290 Chirality : 0.042 0.283 1957 Planarity : 0.004 0.039 2206 Dihedral : 7.356 126.250 1756 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 1.63 % 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: -0.57 (0.22), residues: 1574 helix: 0.66 (0.19), residues: 742 sheet: -1.37 (0.41), residues: 169 loop : -1.24 (0.26), residues: 663 *********************** 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 175 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 167 average time/residue: 0.2108 time to fit residues: 53.9404 Evaluate side-chains 140 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1183 time to fit residues: 4.4257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.8900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12737 Z= 0.201 Angle : 0.645 8.946 17223 Z= 0.307 Chirality : 0.043 0.321 1957 Planarity : 0.004 0.035 2206 Dihedral : 7.327 125.182 1756 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 1.26 % 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: -0.57 (0.22), residues: 1574 helix: 0.50 (0.19), residues: 757 sheet: -1.24 (0.41), residues: 163 loop : -1.12 (0.26), residues: 654 *********************** 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 151 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 144 average time/residue: 0.2274 time to fit residues: 49.3845 Evaluate side-chains 116 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1105 time to fit residues: 3.0677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 GLN C 355 GLN D 359 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.9573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 12737 Z= 0.174 Angle : 0.631 9.801 17223 Z= 0.299 Chirality : 0.042 0.341 1957 Planarity : 0.004 0.036 2206 Dihedral : 7.244 124.210 1756 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 1.26 % 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: -0.36 (0.22), residues: 1574 helix: 0.70 (0.19), residues: 742 sheet: -1.08 (0.42), residues: 162 loop : -1.02 (0.26), residues: 670 *********************** 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 151 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 142 average time/residue: 0.2307 time to fit residues: 49.6632 Evaluate side-chains 126 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1209 time to fit residues: 3.3443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.9798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 12737 Z= 0.150 Angle : 0.644 9.513 17223 Z= 0.302 Chirality : 0.042 0.360 1957 Planarity : 0.004 0.045 2206 Dihedral : 7.113 121.409 1756 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.44 % 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: -0.32 (0.22), residues: 1574 helix: 0.67 (0.19), residues: 760 sheet: -0.91 (0.43), residues: 162 loop : -1.01 (0.26), residues: 652 *********************** 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 128 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 125 average time/residue: 0.2221 time to fit residues: 42.5872 Evaluate side-chains 114 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1392 time to fit residues: 3.3930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 110 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 1.0389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12737 Z= 0.183 Angle : 0.653 8.548 17223 Z= 0.310 Chirality : 0.043 0.372 1957 Planarity : 0.004 0.044 2206 Dihedral : 7.132 119.877 1756 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 0.37 % 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: -0.20 (0.22), residues: 1574 helix: 0.79 (0.19), residues: 745 sheet: -0.99 (0.41), residues: 172 loop : -0.88 (0.26), residues: 657 *********************** 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 122 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.600 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 119 average time/residue: 0.2147 time to fit residues: 40.3682 Evaluate side-chains 112 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.537 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1276 time to fit residues: 2.4893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 1.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12737 Z= 0.215 Angle : 0.678 9.679 17223 Z= 0.321 Chirality : 0.045 0.397 1957 Planarity : 0.004 0.045 2206 Dihedral : 7.202 118.028 1756 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.59 % 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: -0.30 (0.22), residues: 1574 helix: 0.65 (0.19), residues: 745 sheet: -0.95 (0.43), residues: 162 loop : -0.90 (0.26), residues: 667 ********************** 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 111 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.603 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 107 average time/residue: 0.2110 time to fit residues: 35.9110 Evaluate side-chains 99 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1374 time to fit residues: 2.2489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS E 191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.110242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084659 restraints weight = 29339.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084185 restraints weight = 21599.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085126 restraints weight = 17402.966| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 1.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12737 Z= 0.174 Angle : 0.642 10.309 17223 Z= 0.304 Chirality : 0.043 0.366 1957 Planarity : 0.004 0.049 2206 Dihedral : 6.990 112.535 1756 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 0.59 % 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: -0.22 (0.22), residues: 1574 helix: 0.73 (0.19), residues: 750 sheet: -0.88 (0.42), residues: 171 loop : -0.89 (0.26), residues: 653 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2264.32 seconds wall clock time: 42 minutes 21.81 seconds (2541.81 seconds total)