Starting phenix.real_space_refine on Wed Feb 14 19:49:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2024/6rah_4775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2024/6rah_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_2024/6rah_4775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2024/6rah_4775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2024/6rah_4775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rah_4775/02_2024/6rah_4775_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-5238/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: 7.87, per 1000 atoms: 0.77 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: 4.24 Conformation dependent library (CDL) restraints added in 3.0 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: 2.45 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: 3.20 Time building geometry restraints manager: 4.40 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: 5882 16.25 - 32.50: 229 32.50 - 48.75: 55 48.75 - 65.00: 18 65.00 - 81.25: 9 Dihedral angle restraints: 6193 sinusoidal: 2539 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 6190 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 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.850 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.640 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 10.599 81.253 3849 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 % Allowed : 1.82 % Favored : 98.18 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 223 HIS 0.008 0.002 HIS A 554 PHE 0.038 0.003 PHE A 229 TYR 0.019 0.002 TYR A 299 ARG 0.026 0.001 ARG B 88 *********************** 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 : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7570 (mtm110) REVERT: A 259 LEU cc_start: 0.8379 (tt) cc_final: 0.8174 (tp) REVERT: A 467 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 477 GLU cc_start: 0.7534 (pt0) cc_final: 0.7194 (pt0) REVERT: A 534 LYS cc_start: 0.8332 (tttm) cc_final: 0.8129 (ttmt) REVERT: A 537 GLN cc_start: 0.7706 (mt0) cc_final: 0.7496 (mt0) REVERT: A 558 THR cc_start: 0.8439 (m) cc_final: 0.8142 (m) REVERT: B 50 ASP cc_start: 0.7870 (m-30) cc_final: 0.7661 (m-30) REVERT: B 63 LEU cc_start: 0.8028 (mt) cc_final: 0.7797 (mt) REVERT: B 164 TYR cc_start: 0.7160 (m-10) cc_final: 0.6876 (m-10) REVERT: B 184 ASP cc_start: 0.8204 (t0) cc_final: 0.7987 (t0) REVERT: B 299 MET cc_start: 0.7626 (mtm) cc_final: 0.7249 (mtt) REVERT: B 481 GLN cc_start: 0.8438 (mt0) cc_final: 0.8221 (mt0) REVERT: B 510 GLU cc_start: 0.7519 (tt0) cc_final: 0.7091 (tt0) REVERT: B 568 GLU cc_start: 0.7921 (tp30) cc_final: 0.7559 (tp30) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 1.6313 time to fit residues: 432.6566 Evaluate side-chains 179 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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: 1.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 GLN B 202 GLN B 524 GLN B 573 GLN C 32 ASN C 57 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10371 Z= 0.186 Angle : 0.570 8.294 14075 Z= 0.294 Chirality : 0.040 0.157 1604 Planarity : 0.004 0.037 1778 Dihedral : 6.891 78.262 1501 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.49 % Allowed : 12.05 % Favored : 85.47 % 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: 794 sheet: 0.01 (0.42), residues: 129 loop : -1.15 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 223 HIS 0.004 0.001 HIS A 87 PHE 0.025 0.001 PHE B 36 TYR 0.012 0.001 TYR B 302 ARG 0.010 0.001 ARG B 512 *********************** 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 213 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 1.100 Fit side-chains REVERT: A 20 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7543 (mtm110) REVERT: A 99 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7647 (mt0) REVERT: A 334 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: A 425 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7856 (mtp85) REVERT: A 467 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7538 (tm-30) REVERT: A 534 LYS cc_start: 0.8185 (tttm) cc_final: 0.7925 (ttmt) REVERT: A 578 SER cc_start: 0.7489 (m) cc_final: 0.7266 (t) REVERT: A 585 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6713 (ptmm) REVERT: B 11 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7559 (ptp-110) REVERT: B 63 LEU cc_start: 0.8041 (mt) cc_final: 0.7836 (mt) REVERT: B 164 TYR cc_start: 0.7222 (m-10) cc_final: 0.6928 (m-10) REVERT: B 185 ARG cc_start: 0.7541 (ttt-90) cc_final: 0.7269 (mtp85) REVERT: B 189 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 299 MET cc_start: 0.7594 (mtm) cc_final: 0.7174 (mtt) REVERT: B 325 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: B 338 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6963 (mt-10) REVERT: B 372 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7456 (mtp85) REVERT: B 481 GLN cc_start: 0.8498 (mt0) cc_final: 0.8259 (mt0) REVERT: B 568 GLU cc_start: 0.7840 (tp30) cc_final: 0.7553 (tp30) REVERT: C 80 HIS cc_start: 0.6341 (m-70) cc_final: 0.6075 (m-70) REVERT: C 98 THR cc_start: 0.7758 (p) cc_final: 0.7471 (p) outliers start: 26 outliers final: 7 residues processed: 199 average time/residue: 1.5129 time to fit residues: 318.9962 Evaluate side-chains 175 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10371 Z= 0.218 Angle : 0.562 8.917 14075 Z= 0.284 Chirality : 0.039 0.145 1604 Planarity : 0.004 0.049 1778 Dihedral : 6.474 76.602 1501 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.63 % Allowed : 12.62 % Favored : 83.75 % 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: 0.82 (0.23), residues: 1272 helix: 1.23 (0.18), residues: 802 sheet: 0.30 (0.43), residues: 129 loop : -0.89 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 223 HIS 0.004 0.001 HIS A 87 PHE 0.015 0.001 PHE C 37 TYR 0.013 0.001 TYR A 427 ARG 0.016 0.001 ARG B 512 *********************** 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 219 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 1.267 Fit side-chains REVERT: A 48 LEU cc_start: 0.6997 (mp) cc_final: 0.6572 (tp) REVERT: A 106 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.7996 (mp) REVERT: A 127 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7311 (mpp-170) REVERT: A 199 ARG cc_start: 0.7362 (ttp-170) cc_final: 0.6770 (tpp80) REVERT: A 255 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7116 (mtm110) REVERT: A 301 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7341 (mmm-85) REVERT: A 305 GLN cc_start: 0.7748 (mm110) cc_final: 0.7486 (mp10) REVERT: A 313 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7996 (mptm) REVERT: A 334 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: A 354 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: A 425 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7783 (mtt90) REVERT: A 428 ARG cc_start: 0.7235 (mtt90) cc_final: 0.6996 (mtt90) REVERT: A 467 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7347 (tt0) REVERT: A 534 LYS cc_start: 0.8233 (tttm) cc_final: 0.7952 (ttmt) REVERT: B 164 TYR cc_start: 0.7346 (m-10) cc_final: 0.7050 (m-10) REVERT: B 189 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 248 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6642 (tt) REVERT: B 292 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7866 (mp) REVERT: B 568 GLU cc_start: 0.7811 (tp30) cc_final: 0.7541 (tp30) REVERT: C 60 TYR cc_start: 0.8302 (m-80) cc_final: 0.8099 (m-80) REVERT: C 98 THR cc_start: 0.8004 (p) cc_final: 0.7711 (p) REVERT: C 107 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7376 (tpt90) outliers start: 38 outliers final: 12 residues processed: 202 average time/residue: 1.5007 time to fit residues: 321.3317 Evaluate side-chains 184 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.3980 chunk 86 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3376 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= 0.186 Angle : 0.533 9.643 14075 Z= 0.266 Chirality : 0.039 0.140 1604 Planarity : 0.004 0.039 1778 Dihedral : 6.117 77.235 1501 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.44 % Allowed : 14.34 % Favored : 82.22 % 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: 1.31 (0.23), residues: 1272 helix: 1.61 (0.18), residues: 800 sheet: 0.25 (0.42), residues: 134 loop : -0.57 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 223 HIS 0.004 0.001 HIS A 87 PHE 0.025 0.001 PHE B 36 TYR 0.015 0.001 TYR A 541 ARG 0.011 0.000 ARG B 185 *********************** 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 208 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 172 time to evaluate : 1.227 Fit side-chains REVERT: A 12 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.4993 (mtp-110) REVERT: A 48 LEU cc_start: 0.7069 (mp) cc_final: 0.6647 (tp) REVERT: A 127 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7330 (mpp-170) REVERT: A 199 ARG cc_start: 0.7391 (ttp-170) cc_final: 0.6768 (tpp80) REVERT: A 205 MET cc_start: 0.8519 (tmm) cc_final: 0.8315 (tmm) REVERT: A 354 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: A 425 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7769 (mtt90) REVERT: A 467 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7351 (tt0) REVERT: A 534 LYS cc_start: 0.7935 (tttm) cc_final: 0.7452 (ttmt) REVERT: B 35 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7527 (mp) REVERT: B 76 SER cc_start: 0.8047 (t) cc_final: 0.7697 (m) REVERT: B 164 TYR cc_start: 0.7355 (m-10) cc_final: 0.7041 (m-10) REVERT: B 177 ARG cc_start: 0.7175 (mmm160) cc_final: 0.6904 (mmm-85) REVERT: B 248 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6565 (tt) REVERT: B 267 MET cc_start: 0.6516 (mmm) cc_final: 0.5949 (mmm) REVERT: B 372 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7493 (mtp85) REVERT: B 481 GLN cc_start: 0.8554 (mt0) cc_final: 0.8030 (mt0) REVERT: B 549 ARG cc_start: 0.7710 (ptm-80) cc_final: 0.7310 (ptm-80) REVERT: B 568 GLU cc_start: 0.7782 (tp30) cc_final: 0.7555 (tp30) REVERT: C 83 MET cc_start: 0.6319 (mtm) cc_final: 0.6036 (mtm) REVERT: C 98 THR cc_start: 0.8168 (p) cc_final: 0.7874 (p) REVERT: C 107 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7340 (tpt90) outliers start: 36 outliers final: 15 residues processed: 195 average time/residue: 1.5134 time to fit residues: 312.8587 Evaluate side-chains 180 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10371 Z= 0.233 Angle : 0.552 8.033 14075 Z= 0.277 Chirality : 0.040 0.138 1604 Planarity : 0.004 0.050 1778 Dihedral : 6.435 75.823 1501 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.15 % Allowed : 15.30 % Favored : 81.55 % 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: 1.45 (0.23), residues: 1272 helix: 1.71 (0.18), residues: 798 sheet: 0.35 (0.42), residues: 134 loop : -0.49 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 223 HIS 0.004 0.001 HIS A 87 PHE 0.022 0.002 PHE B 36 TYR 0.013 0.001 TYR A 541 ARG 0.012 0.001 ARG B 185 *********************** 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 202 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.136 Fit side-chains REVERT: A 12 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5018 (mtp-110) REVERT: A 48 LEU cc_start: 0.7186 (mp) cc_final: 0.6713 (tp) REVERT: A 127 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7341 (mpp-170) REVERT: A 199 ARG cc_start: 0.7647 (ttp-170) cc_final: 0.6803 (tpp80) REVERT: A 334 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7091 (tp30) REVERT: A 354 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: A 467 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7391 (tt0) REVERT: A 534 LYS cc_start: 0.7866 (tttm) cc_final: 0.7220 (ttmt) REVERT: A 569 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7470 (ttm170) REVERT: B 35 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7314 (mp) REVERT: B 164 TYR cc_start: 0.7403 (m-10) cc_final: 0.7088 (m-10) REVERT: B 177 ARG cc_start: 0.7254 (mmm160) cc_final: 0.7022 (mmm-85) REVERT: B 248 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6712 (tt) REVERT: B 301 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7748 (mp) REVERT: B 325 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: B 372 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7516 (mtp85) REVERT: B 481 GLN cc_start: 0.8541 (mt0) cc_final: 0.8034 (mt0) REVERT: B 549 ARG cc_start: 0.7678 (ptm-80) cc_final: 0.7304 (ptm-80) REVERT: C 65 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8359 (ttpt) REVERT: C 83 MET cc_start: 0.6419 (mtm) cc_final: 0.6066 (mtm) REVERT: C 98 THR cc_start: 0.8050 (p) cc_final: 0.7841 (p) REVERT: C 107 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7358 (tpt90) outliers start: 33 outliers final: 16 residues processed: 188 average time/residue: 1.6196 time to fit residues: 322.5066 Evaluate side-chains 190 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.0770 chunk 110 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3771 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= 0.194 Angle : 0.538 12.162 14075 Z= 0.267 Chirality : 0.039 0.139 1604 Planarity : 0.004 0.056 1778 Dihedral : 6.181 75.900 1501 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.15 % Allowed : 15.49 % Favored : 81.36 % 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: 1.62 (0.23), residues: 1272 helix: 1.81 (0.18), residues: 801 sheet: 0.52 (0.43), residues: 129 loop : -0.39 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 223 HIS 0.004 0.001 HIS A 87 PHE 0.024 0.001 PHE B 36 TYR 0.013 0.001 TYR A 541 ARG 0.013 0.000 ARG B 185 *********************** 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 206 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.249 Fit side-chains REVERT: A 12 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5088 (mtp-110) REVERT: A 48 LEU cc_start: 0.7139 (mp) cc_final: 0.6634 (tp) REVERT: A 111 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8283 (m) REVERT: A 127 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7235 (mpp-170) REVERT: A 199 ARG cc_start: 0.7652 (ttp-170) cc_final: 0.6769 (tpp80) REVERT: A 334 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7006 (tp30) REVERT: A 354 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: A 425 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.7802 (mtt-85) REVERT: A 467 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7462 (tt0) REVERT: A 534 LYS cc_start: 0.7777 (tttm) cc_final: 0.7277 (ttmt) REVERT: A 569 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7431 (ttm170) REVERT: B 11 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.7471 (ptp-110) REVERT: B 35 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7255 (mp) REVERT: B 164 TYR cc_start: 0.7401 (m-10) cc_final: 0.7095 (m-10) REVERT: B 177 ARG cc_start: 0.7334 (mmm160) cc_final: 0.7101 (mmm-85) REVERT: B 181 ARG cc_start: 0.7168 (mtm-85) cc_final: 0.6743 (mtt90) REVERT: B 267 MET cc_start: 0.6587 (mmm) cc_final: 0.5935 (mmm) REVERT: B 301 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7701 (mp) REVERT: B 325 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: B 372 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7502 (mtp85) REVERT: B 481 GLN cc_start: 0.8522 (mt0) cc_final: 0.8010 (mt0) REVERT: B 532 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7269 (mtm110) REVERT: B 549 ARG cc_start: 0.7665 (ptm-80) cc_final: 0.7381 (ptm-80) REVERT: B 557 GLU cc_start: 0.7508 (mp0) cc_final: 0.7148 (mm-30) REVERT: C 65 LYS cc_start: 0.8690 (ttpp) cc_final: 0.8394 (ttpt) REVERT: C 98 THR cc_start: 0.8129 (p) cc_final: 0.7921 (p) REVERT: C 107 ARG cc_start: 0.7947 (tpp80) cc_final: 0.7345 (tpt90) outliers start: 33 outliers final: 16 residues processed: 192 average time/residue: 1.4655 time to fit residues: 298.5627 Evaluate side-chains 189 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3903 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= 0.206 Angle : 0.536 11.232 14075 Z= 0.267 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.054 1778 Dihedral : 6.222 76.248 1501 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.15 % Allowed : 15.97 % Favored : 80.88 % 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: 1.72 (0.24), residues: 1272 helix: 1.85 (0.18), residues: 798 sheet: 0.59 (0.43), residues: 129 loop : -0.25 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 36 HIS 0.004 0.001 HIS A 87 PHE 0.024 0.001 PHE B 36 TYR 0.012 0.001 TYR A 541 ARG 0.012 0.000 ARG B 185 *********************** 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 204 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.5133 (mtp-110) REVERT: A 48 LEU cc_start: 0.7130 (mp) cc_final: 0.6662 (tp) REVERT: A 111 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8281 (m) REVERT: A 127 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7300 (mpp-170) REVERT: A 199 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.6801 (tpp80) REVERT: A 238 LYS cc_start: 0.8558 (mtpm) cc_final: 0.8247 (mttp) REVERT: A 305 GLN cc_start: 0.7670 (mm110) cc_final: 0.7437 (mp10) REVERT: A 334 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: A 354 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: A 425 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.7683 (mtt180) REVERT: A 525 THR cc_start: 0.8573 (p) cc_final: 0.8239 (p) REVERT: A 534 LYS cc_start: 0.7687 (tttm) cc_final: 0.7347 (ttmt) REVERT: A 569 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7447 (ttp-170) REVERT: B 11 ARG cc_start: 0.7852 (ptp-170) cc_final: 0.7486 (ptp-110) REVERT: B 35 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7218 (mp) REVERT: B 164 TYR cc_start: 0.7402 (m-10) cc_final: 0.7132 (m-10) REVERT: B 177 ARG cc_start: 0.7314 (mmm160) cc_final: 0.7108 (mmm-85) REVERT: B 181 ARG cc_start: 0.7187 (mtm-85) cc_final: 0.6760 (mtt90) REVERT: B 267 MET cc_start: 0.6365 (mmm) cc_final: 0.5730 (mtp) REVERT: B 325 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: B 372 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7487 (mtp85) REVERT: B 481 GLN cc_start: 0.8567 (mt0) cc_final: 0.8057 (mt0) REVERT: B 532 ARG cc_start: 0.7539 (mtm180) cc_final: 0.7301 (mtm110) REVERT: B 549 ARG cc_start: 0.7641 (ptm-80) cc_final: 0.7421 (ptm-80) REVERT: B 557 GLU cc_start: 0.7508 (mp0) cc_final: 0.7097 (mm-30) REVERT: C 65 LYS cc_start: 0.8690 (ttpp) cc_final: 0.8398 (ttpt) REVERT: C 107 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7199 (tpt90) outliers start: 33 outliers final: 19 residues processed: 191 average time/residue: 1.5199 time to fit residues: 307.4011 Evaluate side-chains 195 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10371 Z= 0.221 Angle : 0.551 10.660 14075 Z= 0.272 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.051 1778 Dihedral : 6.298 75.428 1501 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.06 % Allowed : 16.54 % Favored : 80.40 % 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: 1.71 (0.23), residues: 1272 helix: 1.83 (0.18), residues: 798 sheet: 0.59 (0.43), residues: 129 loop : -0.22 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 36 HIS 0.004 0.001 HIS A 87 PHE 0.024 0.001 PHE B 36 TYR 0.013 0.001 TYR B 302 ARG 0.012 0.001 ARG B 185 *********************** 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 202 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5130 (mtp-110) REVERT: A 48 LEU cc_start: 0.7126 (mp) cc_final: 0.6636 (tp) REVERT: A 111 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8285 (m) REVERT: A 127 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7305 (mpp-170) REVERT: A 199 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.6831 (tpp80) REVERT: A 238 LYS cc_start: 0.8577 (mtpm) cc_final: 0.8261 (mttp) REVERT: A 277 TYR cc_start: 0.7371 (t80) cc_final: 0.6943 (t80) REVERT: A 334 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: A 354 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: A 425 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.7769 (mtt-85) REVERT: A 525 THR cc_start: 0.8597 (p) cc_final: 0.8288 (p) REVERT: A 534 LYS cc_start: 0.7714 (tttm) cc_final: 0.7340 (ttmt) REVERT: A 569 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7446 (ttp-170) REVERT: B 11 ARG cc_start: 0.7847 (ptp-170) cc_final: 0.7480 (ptp-110) REVERT: B 35 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7166 (mp) REVERT: B 164 TYR cc_start: 0.7473 (m-10) cc_final: 0.7174 (m-10) REVERT: B 181 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6812 (mtt90) REVERT: B 248 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6794 (tt) REVERT: B 267 MET cc_start: 0.6361 (mmm) cc_final: 0.5913 (mmm) REVERT: B 325 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: B 372 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.7498 (mtp85) REVERT: B 481 GLN cc_start: 0.8572 (mt0) cc_final: 0.8061 (mt0) REVERT: B 549 ARG cc_start: 0.7637 (ptm-80) cc_final: 0.7427 (ptm-80) REVERT: B 557 GLU cc_start: 0.7516 (mp0) cc_final: 0.7161 (mm-30) REVERT: C 65 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8404 (ttpt) REVERT: C 83 MET cc_start: 0.6300 (mtm) cc_final: 0.5964 (mtm) REVERT: C 107 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7201 (tpt90) outliers start: 32 outliers final: 20 residues processed: 187 average time/residue: 1.5259 time to fit residues: 302.2531 Evaluate side-chains 197 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 106 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10371 Z= 0.179 Angle : 0.531 10.379 14075 Z= 0.263 Chirality : 0.038 0.139 1604 Planarity : 0.004 0.055 1778 Dihedral : 6.017 76.790 1501 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.77 % Allowed : 17.40 % Favored : 79.83 % 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: 1.88 (0.24), residues: 1272 helix: 1.96 (0.18), residues: 798 sheet: 0.64 (0.44), residues: 129 loop : -0.12 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 36 HIS 0.003 0.001 HIS A 87 PHE 0.025 0.001 PHE B 36 TYR 0.012 0.001 TYR B 302 ARG 0.013 0.000 ARG B 185 *********************** 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 195 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5107 (mtp-110) REVERT: A 48 LEU cc_start: 0.7129 (mp) cc_final: 0.6660 (tp) REVERT: A 111 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8327 (m) REVERT: A 127 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8163 (mmt90) REVERT: A 199 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.6803 (tpp80) REVERT: A 238 LYS cc_start: 0.8566 (mtpm) cc_final: 0.8247 (mttp) REVERT: A 277 TYR cc_start: 0.7358 (t80) cc_final: 0.6934 (t80) REVERT: A 334 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: A 354 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: A 425 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.7757 (mtt-85) REVERT: A 525 THR cc_start: 0.8566 (p) cc_final: 0.8252 (p) REVERT: A 534 LYS cc_start: 0.7670 (tttm) cc_final: 0.7233 (ttpt) REVERT: A 560 ARG cc_start: 0.6050 (mmm160) cc_final: 0.5725 (mtm-85) REVERT: B 11 ARG cc_start: 0.7834 (ptp-170) cc_final: 0.7485 (ptp-110) REVERT: B 164 TYR cc_start: 0.7461 (m-10) cc_final: 0.7124 (m-10) REVERT: B 248 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6689 (tt) REVERT: B 267 MET cc_start: 0.6428 (mmm) cc_final: 0.6036 (mmm) REVERT: B 372 ARG cc_start: 0.7750 (mtp-110) cc_final: 0.7485 (mtp85) REVERT: B 481 GLN cc_start: 0.8553 (mt0) cc_final: 0.8034 (mt0) REVERT: B 532 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7279 (mtm110) REVERT: B 549 ARG cc_start: 0.7618 (ptm-80) cc_final: 0.7411 (ptm-80) REVERT: B 557 GLU cc_start: 0.7450 (mp0) cc_final: 0.7051 (mm-30) REVERT: C 65 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8398 (ttpt) REVERT: C 107 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7213 (tpt90) outliers start: 29 outliers final: 12 residues processed: 183 average time/residue: 1.5849 time to fit residues: 307.4628 Evaluate side-chains 188 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 77 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7900 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10371 Z= 0.205 Angle : 0.547 10.245 14075 Z= 0.272 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.057 1778 Dihedral : 6.133 77.125 1501 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.39 % Allowed : 17.69 % Favored : 79.92 % 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: 1.85 (0.24), residues: 1272 helix: 1.91 (0.18), residues: 798 sheet: 0.71 (0.44), residues: 129 loop : -0.10 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 36 HIS 0.004 0.001 HIS A 87 PHE 0.025 0.001 PHE B 36 TYR 0.012 0.001 TYR A 541 ARG 0.013 0.001 ARG B 185 ********************** 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 194 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.150 Fit side-chains REVERT: A 12 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5101 (mtp-110) REVERT: A 48 LEU cc_start: 0.7138 (mp) cc_final: 0.6645 (tp) REVERT: A 111 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8287 (m) REVERT: A 127 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8177 (mmt90) REVERT: A 199 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.6820 (tpp80) REVERT: A 238 LYS cc_start: 0.8568 (mtpm) cc_final: 0.8254 (mttp) REVERT: A 277 TYR cc_start: 0.7368 (t80) cc_final: 0.6993 (t80) REVERT: A 334 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7045 (tp30) REVERT: A 354 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7445 (tp30) REVERT: A 425 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7768 (mtt-85) REVERT: A 525 THR cc_start: 0.8549 (p) cc_final: 0.8250 (p) REVERT: A 534 LYS cc_start: 0.7759 (tttm) cc_final: 0.6759 (ttmt) REVERT: A 538 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: A 560 ARG cc_start: 0.6048 (mmm160) cc_final: 0.5741 (mtm-85) REVERT: B 11 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7489 (ptp-110) REVERT: B 35 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7088 (mp) REVERT: B 164 TYR cc_start: 0.7545 (m-10) cc_final: 0.7274 (m-10) REVERT: B 181 ARG cc_start: 0.7243 (mtm-85) cc_final: 0.6871 (mtt90) REVERT: B 248 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6738 (tt) REVERT: B 267 MET cc_start: 0.6283 (mmm) cc_final: 0.5952 (mmm) REVERT: B 372 ARG cc_start: 0.7750 (mtp-110) cc_final: 0.7481 (mtp85) REVERT: B 481 GLN cc_start: 0.8576 (mt0) cc_final: 0.8053 (mt0) REVERT: B 532 ARG cc_start: 0.7519 (mtm180) cc_final: 0.7279 (mtm110) REVERT: B 549 ARG cc_start: 0.7628 (ptm-80) cc_final: 0.7427 (ptm-80) REVERT: B 557 GLU cc_start: 0.7432 (mp0) cc_final: 0.7025 (mm-30) REVERT: C 65 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8392 (ttpt) REVERT: C 107 ARG cc_start: 0.7948 (tpp80) cc_final: 0.7213 (tpt90) outliers start: 25 outliers final: 13 residues processed: 183 average time/residue: 1.5658 time to fit residues: 303.3138 Evaluate side-chains 189 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.138730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.104900 restraints weight = 20748.935| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.24 r_work: 0.3037 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4137 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= 0.208 Angle : 0.555 10.083 14075 Z= 0.275 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.057 1778 Dihedral : 6.169 76.890 1501 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.29 % Allowed : 17.78 % Favored : 79.92 % 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: 1.89 (0.24), residues: 1272 helix: 1.92 (0.18), residues: 798 sheet: 0.73 (0.44), residues: 129 loop : -0.03 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 36 HIS 0.004 0.001 HIS A 87 PHE 0.027 0.001 PHE B 36 TYR 0.012 0.001 TYR B 302 ARG 0.013 0.001 ARG B 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5243.48 seconds wall clock time: 92 minutes 48.95 seconds (5568.95 seconds total)