Starting phenix.real_space_refine (version: dev) on Sun Feb 19 14:02:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2023/6rah_4775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2023/6rah_4775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2023/6rah_4775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2023/6rah_4775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2023/6rah_4775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2023/6rah_4775_updated.pdb" } resolution = 2.8 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A ASP 522": "OD1" <-> "OD2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10161 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4690 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 24, 'TRANS': 561} Chain: "B" Number of atoms: 4506 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4499 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} Conformer: "B" Number of residues, atoms: 570, 4499 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} bond proxies already assigned to first conformer: 4579 Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.24, per 1000 atoms: 0.81 Number of scatterers: 10161 At special positions: 0 Unit cell: (103.392, 85.083, 155.088, 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 25 16.00 P 6 15.00 Mg 2 11.99 O 1787 8.00 N 1792 7.00 C 6549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.07 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: 4.78 Conformation dependent library (CDL) restraints added in 2.2 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 9 sheets defined 59.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 13 through 44 removed outlier: 3.983A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Proline residue: A 24 - end of helix removed outlier: 5.557A pdb=" N LEU A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 66 through 119 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.639A pdb=" N ASN A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 172 removed outlier: 3.789A pdb=" N PHE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 221 removed outlier: 3.835A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.521A pdb=" N LEU A 196 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.663A pdb=" N LEU A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 285 removed outlier: 3.553A pdb=" N ARG A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.687A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 331 removed outlier: 3.692A pdb=" N ASP A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Proline residue: A 306 - end of helix removed outlier: 3.977A pdb=" N ASP A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 406 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.967A pdb=" N LEU A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 21 through 54 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 58 through 104 removed outlier: 4.098A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 115 through 132 removed outlier: 3.805A pdb=" N ASP B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 157 Processing helix chain 'B' and resid 159 through 206 removed outlier: 4.287A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.587A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 217 through 268 removed outlier: 3.605A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 4.333A pdb=" N LEU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B 250 " --> pdb=" O HIS B 246 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 316 removed outlier: 4.554A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 4.032A pdb=" N GLY B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 428 through 434 Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 454 through 457 No H-bonds generated for 'chain 'B' and resid 454 through 457' Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 477 through 490 Processing helix chain 'B' and resid 507 through 517 Processing helix chain 'B' and resid 533 through 538 removed outlier: 5.230A pdb=" N HIS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 561 Processing helix chain 'B' and resid 565 through 573 removed outlier: 3.511A pdb=" N GLN B 573 " --> pdb=" O MET B 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 removed outlier: 3.560A pdb=" N LEU C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 381 through 383 Processing sheet with id= B, first strand: chain 'A' and resid 572 through 577 removed outlier: 6.836A pdb=" N VAL A 567 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 565 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER A 549 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A 391 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 551 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLY A 393 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 358 through 360 removed outlier: 7.718A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 359 through 361 Processing sheet with id= E, first strand: chain 'B' and resid 549 through 554 removed outlier: 6.799A pdb=" N VAL B 544 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 553 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 542 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B 526 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE B 369 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 528 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY B 371 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 346 through 348 removed outlier: 6.916A pdb=" N ARG B 348 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TRP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.563A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 118 through 120 removed outlier: 5.675A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 101 through 103 removed outlier: 4.057A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1715 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: 3.27 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1602 1.29 - 1.42: 2713 1.42 - 1.55: 5982 1.55 - 1.68: 29 1.68 - 1.82: 45 Bond restraints: 10371 Sorted by residual: bond pdb=" N HIS B 111 " pdb=" CA BHIS B 111 " ideal model delta sigma weight residual 1.459 1.647 -0.187 1.21e-02 6.83e+03 2.40e+02 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.97e+01 bond pdb=" N PRO C 110 " pdb=" CD PRO C 110 " ideal model delta sigma weight residual 1.473 1.358 0.115 1.40e-02 5.10e+03 6.71e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" N PRO C 88 " pdb=" CD PRO C 88 " ideal model delta sigma weight residual 1.473 1.375 0.098 1.40e-02 5.10e+03 4.87e+01 ... (remaining 10366 not shown) Histogram of bond angle deviations from ideal: 97.67 - 105.34: 257 105.34 - 113.01: 5212 113.01 - 120.67: 5138 120.67 - 128.34: 3381 128.34 - 136.01: 87 Bond angle restraints: 14075 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 121.08 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.23 15.64 1.00e+00 1.00e+00 2.45e+02 angle pdb=" N ALA C 28 " pdb=" CA ALA C 28 " pdb=" C ALA C 28 " ideal model delta sigma weight residual 113.21 131.11 -17.90 1.15e+00 7.56e-01 2.42e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 121.95 14.88 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 123.70 13.13 1.00e+00 1.00e+00 1.73e+02 ... (remaining 14070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 5849 16.25 - 32.50: 218 32.50 - 48.75: 47 48.75 - 65.00: 11 65.00 - 81.25: 6 Dihedral angle restraints: 6131 sinusoidal: 2477 harmonic: 3654 Sorted by residual: dihedral pdb=" C VAL A 59 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " pdb=" CB VAL A 59 " ideal model delta harmonic sigma weight residual -122.00 -137.97 15.97 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" N VAL C 99 " pdb=" C VAL C 99 " pdb=" CA VAL C 99 " pdb=" CB VAL C 99 " ideal model delta harmonic sigma weight residual 123.40 109.91 13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" CA GLY A 151 " pdb=" C GLY A 151 " pdb=" N LEU A 152 " pdb=" CA LEU A 152 " ideal model delta harmonic sigma weight residual -180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 6128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1298 0.096 - 0.193: 214 0.193 - 0.289: 62 0.289 - 0.385: 24 0.385 - 0.482: 6 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.92 -0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA VAL C 99 " pdb=" N VAL C 99 " pdb=" C VAL C 99 " pdb=" CB VAL C 99 " both_signs ideal model delta sigma weight residual False 2.44 2.92 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 1601 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 226 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASP B 226 " 0.070 2.00e-02 2.50e+03 pdb=" O ASP B 226 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU B 227 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 69 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C ARG A 69 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG A 69 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 70 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 223 " -0.021 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP B 223 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 223 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 223 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 223 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 223 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 223 " -0.000 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 65 2.60 - 3.17: 8064 3.17 - 3.75: 15585 3.75 - 4.32: 22202 4.32 - 4.90: 36947 Nonbonded interactions: 82863 Sorted by model distance: nonbonded pdb="MG MG A 702 " pdb=" O HOH A 802 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.047 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.094 2.170 nonbonded pdb=" O2G ATP A 701 " pdb="MG MG A 702 " model vdw 2.102 2.170 nonbonded pdb=" O2B ATP A 701 " pdb="MG MG A 702 " model vdw 2.110 2.170 ... (remaining 82858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 2 5.21 5 S 25 5.16 5 C 6549 2.51 5 N 1792 2.21 5 O 1787 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.160 Process input model: 33.340 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 : 0.008 0.187 10371 Z= 0.527 Angle : 1.529 18.793 14075 Z= 1.082 Chirality : 0.091 0.482 1604 Planarity : 0.007 0.060 1778 Dihedral : 9.898 81.253 3787 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.77 % 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: -2.51 (0.20), residues: 1272 helix: -1.58 (0.15), residues: 778 sheet: -0.29 (0.43), residues: 127 loop : -1.92 (0.27), residues: 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 1.7022 time to fit residues: 452.0733 Evaluate side-chains 175 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN B 202 GLN B 524 GLN B 573 GLN C 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10371 Z= 0.218 Angle : 0.591 8.413 14075 Z= 0.304 Chirality : 0.041 0.158 1604 Planarity : 0.004 0.036 1778 Dihedral : 5.408 86.154 1439 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 2.87 % 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 (0.22), residues: 1272 helix: 0.41 (0.18), residues: 793 sheet: -0.00 (0.42), residues: 129 loop : -1.13 (0.30), residues: 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 1.286 Fit side-chains outliers start: 30 outliers final: 10 residues processed: 205 average time/residue: 1.5111 time to fit residues: 329.1839 Evaluate side-chains 171 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1156 time to fit residues: 2.7137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 537 GLN B 454 HIS B 524 GLN C 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10371 Z= 0.205 Angle : 0.552 8.910 14075 Z= 0.276 Chirality : 0.039 0.144 1604 Planarity : 0.004 0.041 1778 Dihedral : 5.011 84.188 1439 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 3.15 % 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: 0.86 (0.23), residues: 1272 helix: 1.26 (0.18), residues: 801 sheet: 0.16 (0.41), residues: 134 loop : -0.82 (0.32), residues: 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.214 Fit side-chains outliers start: 33 outliers final: 11 residues processed: 187 average time/residue: 1.4624 time to fit residues: 290.7388 Evaluate side-chains 170 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 4 residues processed: 7 average time/residue: 0.3363 time to fit residues: 4.6328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN B 303 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10371 Z= 0.192 Angle : 0.533 6.673 14075 Z= 0.266 Chirality : 0.039 0.146 1604 Planarity : 0.004 0.065 1778 Dihedral : 4.904 85.206 1439 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 2.77 % 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: 1.30 (0.23), residues: 1272 helix: 1.58 (0.18), residues: 803 sheet: 0.36 (0.43), residues: 129 loop : -0.58 (0.32), residues: 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.251 Fit side-chains outliers start: 29 outliers final: 15 residues processed: 186 average time/residue: 1.5853 time to fit residues: 312.6715 Evaluate side-chains 176 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.3337 time to fit residues: 4.2462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN B 191 GLN B 524 GLN C 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 10371 Z= 0.307 Angle : 0.593 8.952 14075 Z= 0.297 Chirality : 0.041 0.138 1604 Planarity : 0.005 0.049 1778 Dihedral : 5.138 84.361 1439 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 3.25 % 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: 1.24 (0.23), residues: 1272 helix: 1.49 (0.18), residues: 802 sheet: 0.66 (0.45), residues: 119 loop : -0.61 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.256 Fit side-chains outliers start: 34 outliers final: 18 residues processed: 190 average time/residue: 1.4932 time to fit residues: 302.5048 Evaluate side-chains 188 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.6102 time to fit residues: 6.5486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN C 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10371 Z= 0.228 Angle : 0.551 7.437 14075 Z= 0.276 Chirality : 0.039 0.139 1604 Planarity : 0.004 0.059 1778 Dihedral : 4.979 84.522 1439 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 2.87 % 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 (0.23), residues: 1272 helix: 1.66 (0.18), residues: 801 sheet: 0.50 (0.44), residues: 124 loop : -0.46 (0.32), residues: 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.298 Fit side-chains outliers start: 30 outliers final: 18 residues processed: 190 average time/residue: 1.5728 time to fit residues: 317.2100 Evaluate side-chains 181 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.4025 time to fit residues: 4.9720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 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 537 GLN C 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10371 Z= 0.211 Angle : 0.550 11.590 14075 Z= 0.272 Chirality : 0.039 0.139 1604 Planarity : 0.004 0.053 1778 Dihedral : 4.905 85.613 1439 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 2.49 % 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: 1.57 (0.23), residues: 1272 helix: 1.75 (0.18), residues: 801 sheet: 0.53 (0.44), residues: 124 loop : -0.35 (0.33), residues: 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.112 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 181 average time/residue: 1.5645 time to fit residues: 301.0244 Evaluate side-chains 178 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.6205 time to fit residues: 5.8537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 96 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10371 Z= 0.203 Angle : 0.535 8.541 14075 Z= 0.267 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.058 1778 Dihedral : 4.869 86.029 1439 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 2.29 % 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: 1.68 (0.23), residues: 1272 helix: 1.82 (0.18), residues: 801 sheet: 0.60 (0.44), residues: 124 loop : -0.26 (0.33), residues: 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.199 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 180 average time/residue: 1.5154 time to fit residues: 289.6648 Evaluate side-chains 178 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.1359 time to fit residues: 2.7059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 103 optimal weight: 0.0470 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN C 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10371 Z= 0.172 Angle : 0.543 13.176 14075 Z= 0.266 Chirality : 0.038 0.138 1604 Planarity : 0.004 0.059 1778 Dihedral : 4.776 88.288 1439 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 1.82 % 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: 1.87 (0.24), residues: 1272 helix: 1.94 (0.18), residues: 800 sheet: 0.72 (0.45), residues: 124 loop : -0.16 (0.33), residues: 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 177 average time/residue: 1.5221 time to fit residues: 287.2130 Evaluate side-chains 175 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1612 time to fit residues: 2.0129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.0000 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10371 Z= 0.210 Angle : 0.551 10.228 14075 Z= 0.272 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.062 1778 Dihedral : 4.826 86.961 1439 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 1.53 % 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: 1.80 (0.24), residues: 1272 helix: 1.86 (0.18), residues: 801 sheet: 0.72 (0.44), residues: 129 loop : -0.15 (0.34), residues: 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 1.260 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 180 average time/residue: 1.5185 time to fit residues: 291.1711 Evaluate side-chains 178 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0961 time to fit residues: 1.8895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104750 restraints weight = 20733.795| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.24 r_work: 0.3045 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10371 Z= 0.216 Angle : 0.575 12.563 14075 Z= 0.281 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.059 1778 Dihedral : 4.846 86.478 1439 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 1.53 % 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: 1.79 (0.24), residues: 1272 helix: 1.85 (0.18), residues: 801 sheet: 0.69 (0.44), residues: 129 loop : -0.11 (0.34), residues: 342 =============================================================================== Job complete usr+sys time: 5023.42 seconds wall clock time: 89 minutes 40.33 seconds (5380.33 seconds total)