Starting phenix.real_space_refine (version: 1.19rc7) on Sun Dec 6 18:43:05 2020 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqn_22290/12_2020/6xqn_22290.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqn_22290/12_2020/6xqn_22290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqn_22290/12_2020/6xqn_22290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqn_22290/12_2020/6xqn_22290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqn_22290/12_2020/6xqn_22290.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqn_22290/12_2020/6xqn_22290.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.002 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 9433 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 223 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1166 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1128 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "G" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 174 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1156 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 186 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1137 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "I" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2243 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 185 Chain: "J" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2019 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 4, 'TRANS': 286} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 12, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 254 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.90, per 1000 atoms: 0.63 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 178 through 194 or (resid 195 through 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 20 \ 5 or (resid 206 and (name N or name CA or name C or name O or name CB )) or resi \ d 207 through 219 or (resid 220 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD )) or resid 221 through 251 or (resid 252 and (name \ N or name CA or name C or name O or name CB )) or resid 253 through 256 or (resi \ d 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thro \ ugh 299 or (resid 300 and (name N or name CA or name C or name O or name CB )) o \ r resid 312 through 327 or (resid 328 and (name N or name CA or name C or name O \ or name CB )) or resid 329 through 336)) selection = (chain 'B' and (resid 178 through 251 or (resid 252 and (name N or name CA or na \ me C or name O or name CB )) or resid 253 through 256 or (resid 257 and (name N \ or name CA or name C or name O or name CB )) or resid 258 through 286 or resid 2 \ 92 through 336)) selection = (chain 'C' and (resid 178 through 194 or (resid 195 through 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 20 \ 5 or (resid 206 and (name N or name CA or name C or name O or name CB )) or resi \ d 207 through 219 or (resid 220 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD )) or resid 221 through 299 or (resid 300 and (name \ N or name CA or name C or name O or name CB )) or resid 312 through 327 or (resi \ d 328 and (name N or name CA or name C or name O or name CB )) or resid 329 thro \ ugh 336)) selection = (chain 'D' and (resid 178 through 191 or (resid 192 through 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 20 \ 5 or (resid 206 and (name N or name CA or name C or name O or name CB )) or resi \ d 207 through 251 or (resid 252 and (name N or name CA or name C or name O or na \ me CB )) or resid 253 through 256 or (resid 257 and (name N or name CA or name C \ or name O or name CB )) or resid 258 through 286 or resid 292 through 336)) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 68 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 92)) } Number of scatterers: 9433 At special positions: 0 Unit cell: (86.184, 112.784, 165.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 37 16.00 O 1664 8.00 N 1561 7.00 C 6170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 2 sheets defined 80.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'E' and resid 65 through 95 removed outlier: 4.326A pdb=" N ARG E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) Proline residue: E 76 - end of helix Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 194 through 254 removed outlier: 3.788A pdb=" N GLN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 4.083A pdb=" N ARG A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.627A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 313 through 336 Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 194 through 256 removed outlier: 3.542A pdb=" N LYS B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 4.426A pdb=" N ARG B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 300 removed outlier: 3.514A pdb=" N THR B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 336 removed outlier: 3.538A pdb=" N ASP B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 Proline residue: G 76 - end of helix Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 194 through 256 removed outlier: 3.734A pdb=" N GLN C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.765A pdb=" N ARG C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 285 Processing helix chain 'C' and resid 293 through 308 Processing helix chain 'C' and resid 313 through 336 Processing helix chain 'H' and resid 68 through 92 Proline residue: H 76 - end of helix Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 197 through 256 Proline residue: D 216 - end of helix removed outlier: 4.057A pdb=" N ARG D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 300 removed outlier: 3.873A pdb=" N THR D 267 " --> pdb=" O MET D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 336 removed outlier: 3.541A pdb=" N TYR D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 122 Processing helix chain 'I' and resid 125 through 132 Processing helix chain 'I' and resid 148 through 155 Processing helix chain 'I' and resid 193 through 199 removed outlier: 3.767A pdb=" N GLY I 199 " --> pdb=" O TYR I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 218 removed outlier: 3.563A pdb=" N PHE I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER I 217 " --> pdb=" O THR I 213 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR I 218 " --> pdb=" O THR I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 230 removed outlier: 3.638A pdb=" N PHE I 223 " --> pdb=" O PRO I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 253 Processing helix chain 'I' and resid 278 through 284 Processing helix chain 'I' and resid 292 through 314 Processing helix chain 'I' and resid 323 through 333 Processing helix chain 'I' and resid 339 through 351 Processing helix chain 'I' and resid 360 through 372 Processing helix chain 'I' and resid 373 through 388 removed outlier: 3.573A pdb=" N GLY I 388 " --> pdb=" O TYR I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 405 Processing helix chain 'I' and resid 409 through 419 removed outlier: 3.552A pdb=" N CYS I 413 " --> pdb=" O SER I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 442 Processing helix chain 'J' and resid 87 through 94 Processing helix chain 'J' and resid 105 through 115 Processing helix chain 'J' and resid 128 through 136 removed outlier: 3.941A pdb=" N LEU J 136 " --> pdb=" O ILE J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 153 Processing helix chain 'J' and resid 159 through 172 Processing helix chain 'J' and resid 174 through 185 removed outlier: 3.517A pdb=" N HIS J 178 " --> pdb=" O HIS J 174 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP J 185 " --> pdb=" O PHE J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 205 Processing helix chain 'J' and resid 232 through 240 Processing helix chain 'J' and resid 248 through 273 removed outlier: 3.639A pdb=" N PHE J 252 " --> pdb=" O HIS J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 289 Processing helix chain 'J' and resid 295 through 306 removed outlier: 3.809A pdb=" N TYR J 299 " --> pdb=" O ASN J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 327 Processing helix chain 'J' and resid 328 through 342 Processing helix chain 'J' and resid 346 through 359 Processing helix chain 'J' and resid 363 through 374 Processing helix chain 'J' and resid 383 through 397 Processing sheet with id=AA1, first strand: chain 'I' and resid 144 through 146 removed outlier: 6.318A pdb=" N LYS I 135 " --> pdb=" O LYS I 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 101 through 103 786 hydrogen bonds defined for protein. 2337 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: 2.83 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2989 1.34 - 1.46: 1831 1.46 - 1.58: 4722 1.58 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 9611 Sorted by residual: bond pdb=" N LYS A 308 " pdb=" CA LYS A 308 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.52e-02 4.33e+03 5.97e+00 bond pdb=" N LYS C 308 " pdb=" CA LYS C 308 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.46e-02 4.69e+03 5.87e+00 bond pdb=" C ALA A 307 " pdb=" N LYS A 308 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.40e-02 5.10e+03 1.50e+00 bond pdb=" C ALA C 307 " pdb=" N LYS C 308 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.45e-02 4.76e+03 1.37e+00 bond pdb=" CG LEU J 184 " pdb=" CD2 LEU J 184 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 ... (remaining 9606 not shown) Histogram of bond angle deviations from ideal: 98.38 - 105.51: 106 105.51 - 112.65: 5222 112.65 - 119.78: 2999 119.78 - 126.92: 4683 126.92 - 134.05: 93 Bond angle restraints: 13103 Sorted by residual: angle pdb=" N ARG I 129 " pdb=" CA ARG I 129 " pdb=" CB ARG I 129 " ideal model delta sigma weight residual 110.32 119.55 -9.23 1.70e+00 3.46e-01 2.95e+01 angle pdb=" N LEU J 328 " pdb=" CA LEU J 328 " pdb=" C LEU J 328 " ideal model delta sigma weight residual 112.34 118.26 -5.92 1.30e+00 5.92e-01 2.07e+01 angle pdb=" CA LEU G 92 " pdb=" CB LEU G 92 " pdb=" CG LEU G 92 " ideal model delta sigma weight residual 116.30 125.32 -9.02 3.50e+00 8.16e-02 6.64e+00 angle pdb=" CA LEU H 92 " pdb=" CB LEU H 92 " pdb=" CG LEU H 92 " ideal model delta sigma weight residual 116.30 125.15 -8.85 3.50e+00 8.16e-02 6.39e+00 angle pdb=" C THR D 254 " pdb=" N TRP D 255 " pdb=" CA TRP D 255 " ideal model delta sigma weight residual 122.26 118.46 3.80 1.59e+00 3.96e-01 5.71e+00 ... (remaining 13098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4984 17.62 - 35.25: 485 35.25 - 52.87: 87 52.87 - 70.49: 12 70.49 - 88.12: 7 Dihedral angle restraints: 5575 sinusoidal: 1800 harmonic: 3775 Sorted by residual: dihedral pdb=" CA ALA A 307 " pdb=" C ALA A 307 " pdb=" N LYS A 308 " pdb=" CA LYS A 308 " ideal model delta harmonic sigma weight residual 180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" N ARG I 129 " pdb=" C ARG I 129 " pdb=" CA ARG I 129 " pdb=" CB ARG I 129 " ideal model delta harmonic sigma weight residual 122.80 133.74 -10.94 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" CA HIS J 327 " pdb=" C HIS J 327 " pdb=" N LEU J 328 " pdb=" CA LEU J 328 " ideal model delta harmonic sigma weight residual -180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1440 0.069 - 0.137: 147 0.137 - 0.206: 5 0.206 - 0.274: 0 0.274 - 0.343: 1 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CA ARG I 129 " pdb=" N ARG I 129 " pdb=" C ARG I 129 " pdb=" CB ARG I 129 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL I 416 " pdb=" CA VAL I 416 " pdb=" CG1 VAL I 416 " pdb=" CG2 VAL I 416 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB ILE J 366 " pdb=" CA ILE J 366 " pdb=" CG1 ILE J 366 " pdb=" CG2 ILE J 366 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1590 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 196 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C GLN B 196 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN B 196 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 197 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 307 " 0.014 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C ALA C 307 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA C 307 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 308 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 307 " 0.014 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C ALA A 307 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA A 307 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 308 " 0.015 2.00e-02 2.50e+03 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 32 2.52 - 3.11: 7273 3.11 - 3.71: 14654 3.71 - 4.30: 18389 4.30 - 4.90: 31150 Nonbonded interactions: 71498 Sorted by model distance: nonbonded pdb=" OE2 GLU C 264 " pdb="CA CA B 401 " model vdw 1.922 2.660 nonbonded pdb=" OE2 GLU D 264 " pdb="CA CA B 401 " model vdw 1.978 2.660 nonbonded pdb=" OE2 GLU A 264 " pdb="CA CA B 401 " model vdw 2.132 2.660 nonbonded pdb=" OE2 GLU B 264 " pdb="CA CA B 401 " model vdw 2.139 2.660 nonbonded pdb=" OH TYR B 272 " pdb=" OE1 GLN C 246 " model vdw 2.229 2.440 ... (remaining 71493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 9433 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 37 5.16 5 C 6170 2.51 5 N 1561 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set model interpretation parameters: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.660 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.040 Process input model: 30.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 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:2.170 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.038 9611 Angle : 0.666 9.232 13103 Chirality : 0.041 0.343 1593 Planarity : 0.004 0.043 1632 Dihedral : 14.562 88.119 3117 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.22), residues: 1256 helix: 0.79 (0.15), residues: 991 sheet: -4.08 (0.89), residues: 9 loop : -2.39 (0.30), residues: 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 24 poor density : 265 time to evaluate : 1.096 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 285 average time/residue: 0.2429 time to fit residues: 71.1599 Evaluate side-chains 185 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 10 poor density : 175 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0943 time to fit residues: 2.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 226 GLN A 315 ASN I 159 ASN ** I 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS J 393 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.033 9611 Angle : 0.539 7.756 13103 Chirality : 0.035 0.122 1593 Planarity : 0.003 0.039 1632 Dihedral : 3.834 24.170 1355 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.23), residues: 1256 helix: 2.38 (0.16), residues: 1021 sheet: -0.36 (2.21), residues: 8 loop : -2.11 (0.32), residues: 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2084 time to fit residues: 49.7982 Evaluate side-chains 171 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 315 ASN I 159 ASN ** I 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.035 9611 Angle : 0.511 6.920 13103 Chirality : 0.035 0.132 1593 Planarity : 0.003 0.042 1632 Dihedral : 3.661 23.230 1355 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.06 (0.24), residues: 1256 helix: 2.84 (0.16), residues: 1018 sheet: -0.65 (2.16), residues: 8 loop : -1.94 (0.33), residues: 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 205 time to evaluate : 1.153 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.2110 time to fit residues: 45.4538 Evaluate side-chains 166 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 385 HIS J 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.028 9611 Angle : 0.503 6.703 13103 Chirality : 0.034 0.124 1593 Planarity : 0.003 0.042 1632 Dihedral : 3.495 21.462 1355 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.28 (0.24), residues: 1256 helix: 2.99 (0.16), residues: 1019 sheet: -0.56 (2.27), residues: 8 loop : -1.86 (0.33), residues: 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 198 time to evaluate : 1.298 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.2025 time to fit residues: 42.3063 Evaluate side-chains 165 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN I 247 GLN I 385 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.032 9611 Angle : 0.500 7.071 13103 Chirality : 0.035 0.141 1593 Planarity : 0.003 0.040 1632 Dihedral : 3.481 18.247 1355 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.38 (0.24), residues: 1256 helix: 3.04 (0.16), residues: 1019 sheet: -0.66 (2.30), residues: 8 loop : -1.73 (0.34), residues: 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.155 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2026 time to fit residues: 41.6391 Evaluate side-chains 164 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 211 GLN I 385 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.031 9611 Angle : 0.499 6.864 13103 Chirality : 0.035 0.127 1593 Planarity : 0.003 0.041 1632 Dihedral : 3.444 15.640 1355 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.41 (0.24), residues: 1256 helix: 3.06 (0.16), residues: 1019 sheet: -0.90 (2.29), residues: 8 loop : -1.72 (0.34), residues: 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2023 time to fit residues: 41.1974 Evaluate side-chains 158 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN I 385 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.039 9611 Angle : 0.483 6.779 13103 Chirality : 0.034 0.141 1593 Planarity : 0.003 0.041 1632 Dihedral : 3.355 14.944 1355 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.55 (0.24), residues: 1256 helix: 3.14 (0.16), residues: 1020 sheet: -0.90 (2.34), residues: 8 loop : -1.61 (0.35), residues: 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.320 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2137 time to fit residues: 42.1713 Evaluate side-chains 157 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 0.4980 chunk 77 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 385 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.043 9611 Angle : 0.515 6.909 13103 Chirality : 0.035 0.137 1593 Planarity : 0.003 0.040 1632 Dihedral : 3.344 14.304 1355 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.50 (0.24), residues: 1256 helix: 3.10 (0.16), residues: 1025 sheet: -1.07 (2.32), residues: 8 loop : -1.68 (0.34), residues: 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.105 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2122 time to fit residues: 41.7994 Evaluate side-chains 153 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 chunk 107 optimal weight: 30.0000 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN I 385 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.048 9611 Angle : 0.561 7.756 13103 Chirality : 0.036 0.139 1593 Planarity : 0.003 0.037 1632 Dihedral : 3.479 15.149 1355 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.33 (0.24), residues: 1256 helix: 2.99 (0.16), residues: 1022 sheet: -1.32 (2.29), residues: 8 loop : -1.68 (0.34), residues: 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2090 time to fit residues: 39.6391 Evaluate side-chains 147 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 159 ASN I 385 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.059 9611 Angle : 0.551 7.262 13103 Chirality : 0.036 0.138 1593 Planarity : 0.003 0.038 1632 Dihedral : 3.451 14.237 1355 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.39 (0.24), residues: 1256 helix: 3.04 (0.16), residues: 1023 sheet: -1.43 (2.25), residues: 8 loop : -1.71 (0.34), residues: 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield and 0 Emsley and 1256 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.156 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2079 time to fit residues: 38.1310 Evaluate side-chains 151 residues out of total 1153 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 385 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.211294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.171557 restraints weight = 14531.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.173018 restraints weight = 9045.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.173164 restraints weight = 6423.215| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.003 0.046 9611 ANGLE : 0.533 9.328 13103 CHIRALITY : 0.035 0.159 1593 PLANARITY : 0.003 0.038 1632 DIHEDRAL : 3.386 14.811 1355 MIN NONBONDED DISTANCE : 2.184 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 6.41 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.59 % FAVORED : 98.41 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % 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: 3.52 (0.24), RESIDUES: 1256 HELIX: 3.15 (0.16), RESIDUES: 1015 SHEET: -1.57 (2.20), RESIDUES: 8 LOOP : -1.64 (0.34), RESIDUES: 233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.046 9611 Angle : 0.533 9.328 13103 Chirality : 0.035 0.159 1593 Planarity : 0.003 0.038 1632 Dihedral : 3.386 14.811 1355 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.52 (0.24), residues: 1256 helix: 3.15 (0.16), residues: 1015 sheet: -1.57 (2.20), residues: 8 loop : -1.64 (0.34), residues: 233 =============================================================================== Job complete usr+sys time: 1918.25 seconds wall clock time: 35 minutes 18.40 seconds (2118.40 seconds total)