Starting phenix.real_space_refine (version: dev) on Tue Apr 5 09:09:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/04_2022/7kch_22808_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/04_2022/7kch_22808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/04_2022/7kch_22808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/04_2022/7kch_22808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/04_2022/7kch_22808_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/04_2022/7kch_22808_updated.pdb" } resolution = 4.33 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 12248 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "A" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 3365 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 592} Link IDs: {'PTRANS': 21, 'TRANS': 658} Chain breaks: 8 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 2164 Unresolved non-hydrogen angles: 2757 Unresolved non-hydrogen dihedrals: 1796 Unresolved non-hydrogen chiralities: 187 Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 19, 'TYR:plan': 20, 'ASN:plan1': 34, 'TRP:plan': 4, 'ASP:plan': 36, 'PHE:plan': 39, 'GLU:plan': 52, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1224 Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" 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: "B" 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: "C" 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} Time building chain proxies: 7.42, per 1000 atoms: 0.61 Number of scatterers: 12248 At special positions: 0 Unit cell: (123.848, 144.672, 140.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 6 15.00 Mg 3 11.99 O 2405 8.00 N 2174 7.00 C 7597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 2.2 seconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 18 sheets defined 41.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 126 removed outlier: 3.705A pdb=" N MET G 123 " --> pdb=" O MET G 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 182 through 196 removed outlier: 3.638A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 215 removed outlier: 3.882A pdb=" N GLU G 207 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG G 210 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 229 Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 252 through 254 No H-bonds generated for 'chain 'G' and resid 252 through 254' Processing helix chain 'G' and resid 256 through 262 removed outlier: 3.963A pdb=" N THR G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU G 261 " --> pdb=" O CYS G 257 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE G 262 " --> pdb=" O PRO G 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 256 through 262' Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 291 through 295 removed outlier: 3.754A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 291 through 295' Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.606A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP G 340 " --> pdb=" O TYR G 337 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU G 346 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA G 347 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 373 removed outlier: 4.284A pdb=" N LYS G 373 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 191 through 206 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.586A pdb=" N GLU A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 394 through 424 removed outlier: 3.597A pdb=" N ASP A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 480 Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 575 through 582 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 616 through 633 removed outlier: 3.798A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 664 Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 684 through 694 Processing helix chain 'A' and resid 710 through 717 Processing helix chain 'A' and resid 736 through 747 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.705A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.637A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.882A pdb=" N GLU B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 256 through 262 removed outlier: 3.962A pdb=" N THR B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 262' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.754A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 295' Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.606A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 4.284A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.704A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.638A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.883A pdb=" N GLU C 207 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.962A pdb=" N THR C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 262' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 291 through 295 removed outlier: 3.755A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 295' Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.606A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 4.284A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'G' and resid 35 through 38 removed outlier: 3.603A pdb=" N ARG G 37 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 103 through 105 Processing sheet with id= D, first strand: chain 'G' and resid 298 through 300 removed outlier: 3.548A pdb=" N SER G 155 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP G 154 " --> pdb=" O HIS G 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.693A pdb=" N LYS G 238 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.100A pdb=" N GLN A 154 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 156 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 437 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 158 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 432 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN A 228 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 539 through 541 Processing sheet with id= H, first strand: chain 'A' and resid 680 through 683 Processing sheet with id= I, first strand: chain 'B' and resid 8 through 11 Processing sheet with id= J, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.603A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= L, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.547A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.692A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= O, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.603A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= Q, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.548A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C 154 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.693A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1299 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: 3.66 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3964 1.33 - 1.45: 1731 1.45 - 1.57: 6616 1.57 - 1.68: 9 1.68 - 1.80: 111 Bond restraints: 12431 Sorted by residual: bond pdb=" C GLY C 150 " pdb=" N ILE C 151 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" C GLY G 150 " pdb=" N ILE G 151 " ideal model delta sigma weight residual 1.333 1.293 0.040 1.20e-02 6.94e+03 1.12e+01 bond pdb=" C GLY B 150 " pdb=" N ILE B 151 " ideal model delta sigma weight residual 1.333 1.293 0.039 1.20e-02 6.94e+03 1.08e+01 bond pdb=" C VAL B 163 " pdb=" N PRO B 164 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.28e-02 6.10e+03 9.01e+00 bond pdb=" C VAL G 163 " pdb=" N PRO G 164 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.28e-02 6.10e+03 8.80e+00 ... (remaining 12426 not shown) Histogram of bond angle deviations from ideal: 98.83 - 106.18: 324 106.18 - 113.53: 7083 113.53 - 120.88: 5826 120.88 - 128.23: 3662 128.23 - 135.58: 83 Bond angle restraints: 16978 Sorted by residual: angle pdb=" C LEU C 94 " pdb=" N ARG C 95 " pdb=" CA ARG C 95 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C LEU B 94 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C LEU G 94 " pdb=" N ARG G 95 " pdb=" CA ARG G 95 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ASN C 162 " pdb=" N VAL C 163 " pdb=" CA VAL C 163 " ideal model delta sigma weight residual 123.33 119.79 3.54 8.70e-01 1.32e+00 1.65e+01 angle pdb=" C ASN B 162 " pdb=" N VAL B 163 " pdb=" CA VAL B 163 " ideal model delta sigma weight residual 123.33 119.82 3.51 8.70e-01 1.32e+00 1.63e+01 ... (remaining 16973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 7241 34.14 - 68.29: 168 68.29 - 102.43: 3 102.43 - 136.57: 9 136.57 - 170.72: 6 Dihedral angle restraints: 7427 sinusoidal: 2214 harmonic: 5213 Sorted by residual: dihedral pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" N9 ADP C 401 " pdb=" C4 ADP C 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.73 -170.72 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP G 401 " pdb=" C1' ADP G 401 " pdb=" N9 ADP G 401 " pdb=" C4 ADP G 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.75 -170.70 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP B 401 " pdb=" C1' ADP B 401 " pdb=" N9 ADP B 401 " pdb=" C4 ADP B 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.79 -170.66 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 7424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1243 0.048 - 0.095: 571 0.095 - 0.143: 161 0.143 - 0.191: 26 0.191 - 0.238: 9 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CB ILE B 34 " pdb=" CA ILE B 34 " pdb=" CG1 ILE B 34 " pdb=" CG2 ILE B 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE G 34 " pdb=" CA ILE G 34 " pdb=" CG1 ILE G 34 " pdb=" CG2 ILE G 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE C 34 " pdb=" CA ILE C 34 " pdb=" CG1 ILE C 34 " pdb=" CG2 ILE C 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2007 not shown) Planarity restraints: 2252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 257 " -0.053 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 258 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS G 257 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO G 258 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 258 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 258 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 257 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO C 258 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.045 5.00e-02 4.00e+02 ... (remaining 2249 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1352 2.72 - 3.26: 12257 3.26 - 3.81: 20477 3.81 - 4.35: 21794 4.35 - 4.90: 36928 Nonbonded interactions: 92808 Sorted by model distance: nonbonded pdb=" O ASN B 297 " pdb=" OD1 ASN B 297 " model vdw 2.175 3.040 nonbonded pdb=" O ASN G 297 " pdb=" OD1 ASN G 297 " model vdw 2.176 3.040 nonbonded pdb=" O ASN C 297 " pdb=" OD1 ASN C 297 " model vdw 2.176 3.040 nonbonded pdb=" CB MET G 47 " pdb=" NH2 ARG C 147 " model vdw 2.215 3.520 nonbonded pdb=" O SER C 155 " pdb=" OG1 THR C 303 " model vdw 2.241 2.440 ... (remaining 92803 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 'B' selection = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 7597 2.51 5 N 2174 2.21 5 O 2405 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 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: 7.690 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: 27.120 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.100 Process input model: 37.650 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5178 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 : 0.011 0.063 12431 Z= 0.770 Angle : 1.074 12.124 16978 Z= 0.619 Chirality : 0.057 0.238 2010 Planarity : 0.008 0.079 2252 Dihedral : 16.548 170.718 4055 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer Outliers : 4.72 % 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: -4.19 (0.16), residues: 1781 helix: -2.75 (0.12), residues: 761 sheet: -1.81 (0.31), residues: 257 loop : -3.06 (0.20), residues: 763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 351 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 12 residues processed: 380 average time/residue: 0.2248 time to fit residues: 123.7275 Evaluate side-chains 227 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1081 time to fit residues: 4.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 0.0670 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 54 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 40.0000 chunk 162 optimal weight: 0.6980 overall best weight: 1.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 GLN B 78 ASN B 101 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN C 73 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS C 246 GLN C 353 GLN C 371 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 12431 Z= 0.324 Angle : 0.833 16.065 16978 Z= 0.415 Chirality : 0.048 0.233 2010 Planarity : 0.006 0.065 2252 Dihedral : 12.559 175.228 1931 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.42 % 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: -2.26 (0.18), residues: 1781 helix: -0.63 (0.17), residues: 773 sheet: -1.63 (0.30), residues: 276 loop : -2.32 (0.22), residues: 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 242 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 245 average time/residue: 0.2223 time to fit residues: 79.7896 Evaluate side-chains 168 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1056 time to fit residues: 2.0281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 135 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 44 optimal weight: 50.0000 chunk 162 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 161 optimal weight: 0.0020 chunk 55 optimal weight: 10.0000 chunk 130 optimal weight: 0.0570 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 ASN ** G 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 280 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 12431 Z= 0.156 Angle : 0.600 9.225 16978 Z= 0.297 Chirality : 0.044 0.144 2010 Planarity : 0.004 0.050 2252 Dihedral : 12.160 177.387 1931 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: -1.43 (0.19), residues: 1781 helix: 0.15 (0.18), residues: 796 sheet: -1.30 (0.30), residues: 279 loop : -2.02 (0.22), residues: 706 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2337 time to fit residues: 74.1842 Evaluate side-chains 155 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 109 optimal weight: 0.3980 chunk 163 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 154 optimal weight: 0.0970 chunk 46 optimal weight: 9.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 HIS ** G 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 1.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 12431 Z= 0.402 Angle : 0.890 15.981 16978 Z= 0.445 Chirality : 0.050 0.247 2010 Planarity : 0.006 0.070 2252 Dihedral : 12.446 171.187 1931 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.42 % 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: -1.29 (0.20), residues: 1781 helix: 0.31 (0.19), residues: 778 sheet: -1.23 (0.29), residues: 287 loop : -1.96 (0.23), residues: 716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.864 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 148 average time/residue: 0.2283 time to fit residues: 53.2542 Evaluate side-chains 103 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1104 time to fit residues: 2.4380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 40.0000 chunk 2 optimal weight: 0.0270 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 147 optimal weight: 0.0370 chunk 119 optimal weight: 0.0770 chunk 0 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 43 optimal weight: 0.0270 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 1.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 12431 Z= 0.142 Angle : 0.591 10.926 16978 Z= 0.289 Chirality : 0.044 0.224 2010 Planarity : 0.004 0.046 2252 Dihedral : 11.775 178.007 1931 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: -0.74 (0.20), residues: 1781 helix: 0.89 (0.20), residues: 768 sheet: -1.04 (0.32), residues: 260 loop : -1.74 (0.22), residues: 753 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.577 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2085 time to fit residues: 44.5822 Evaluate side-chains 105 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 50.0000 chunk 42 optimal weight: 40.0000 chunk 173 optimal weight: 3.9990 chunk 143 optimal weight: 0.0770 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 1.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 12431 Z= 0.302 Angle : 0.704 17.240 16978 Z= 0.342 Chirality : 0.046 0.276 2010 Planarity : 0.004 0.049 2252 Dihedral : 11.845 178.822 1931 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % 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: -0.56 (0.21), residues: 1781 helix: 1.13 (0.20), residues: 754 sheet: -0.93 (0.31), residues: 284 loop : -1.73 (0.23), residues: 743 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.521 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1853 time to fit residues: 35.0672 Evaluate side-chains 90 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 40.0000 chunk 126 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 96 optimal weight: 50.0000 chunk 172 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 40 HIS G 121 GLN B 73 HIS B 173 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 1.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 12431 Z= 0.349 Angle : 0.717 15.889 16978 Z= 0.349 Chirality : 0.047 0.223 2010 Planarity : 0.004 0.044 2252 Dihedral : 12.076 179.123 1931 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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: -0.62 (0.21), residues: 1781 helix: 1.10 (0.20), residues: 769 sheet: -0.94 (0.32), residues: 260 loop : -1.84 (0.22), residues: 752 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.506 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1799 time to fit residues: 33.2172 Evaluate side-chains 86 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 0.0000 chunk 103 optimal weight: 6.9990 chunk 51 optimal weight: 40.0000 chunk 33 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 1.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12431 Z= 0.161 Angle : 0.600 12.760 16978 Z= 0.286 Chirality : 0.044 0.177 2010 Planarity : 0.003 0.039 2252 Dihedral : 11.742 179.616 1931 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % 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: -0.38 (0.21), residues: 1781 helix: 1.23 (0.20), residues: 767 sheet: -0.77 (0.34), residues: 254 loop : -1.65 (0.22), residues: 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.625 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2023 time to fit residues: 38.4818 Evaluate side-chains 90 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 1.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 12431 Z= 0.276 Angle : 0.659 14.298 16978 Z= 0.316 Chirality : 0.045 0.197 2010 Planarity : 0.004 0.039 2252 Dihedral : 11.787 179.292 1931 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % 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: -0.36 (0.21), residues: 1781 helix: 1.28 (0.20), residues: 767 sheet: -0.74 (0.34), residues: 260 loop : -1.68 (0.23), residues: 754 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1835 time to fit residues: 32.3441 Evaluate side-chains 82 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 0.3980 chunk 87 optimal weight: 0.1980 chunk 112 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 1.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 12431 Z= 0.137 Angle : 0.587 11.801 16978 Z= 0.280 Chirality : 0.043 0.183 2010 Planarity : 0.003 0.040 2252 Dihedral : 11.486 175.163 1931 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -0.18 (0.21), residues: 1781 helix: 1.42 (0.20), residues: 750 sheet: -0.63 (0.34), residues: 252 loop : -1.51 (0.22), residues: 779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.422 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1887 time to fit residues: 37.8901 Evaluate side-chains 86 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 40.0000 chunk 130 optimal weight: 0.0040 chunk 20 optimal weight: 0.0970 chunk 39 optimal weight: 50.0000 chunk 142 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.050213 restraints weight = 65749.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.051481 restraints weight = 39634.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052363 restraints weight = 27183.891| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 1.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 12431 Z= 0.153 Angle : 0.581 11.487 16978 Z= 0.275 Chirality : 0.043 0.196 2010 Planarity : 0.003 0.039 2252 Dihedral : 11.285 172.073 1931 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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: -0.17 (0.21), residues: 1781 helix: 1.42 (0.20), residues: 774 sheet: -0.53 (0.34), residues: 252 loop : -1.62 (0.22), residues: 755 =============================================================================== Job complete usr+sys time: 2454.44 seconds wall clock time: 45 minutes 26.37 seconds (2726.37 seconds total)