Starting phenix.real_space_refine on Tue Dec 31 06:31:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gc3_51228/12_2024/9gc3_51228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gc3_51228/12_2024/9gc3_51228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gc3_51228/12_2024/9gc3_51228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gc3_51228/12_2024/9gc3_51228.map" model { file = "/net/cci-nas-00/data/ceres_data/9gc3_51228/12_2024/9gc3_51228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gc3_51228/12_2024/9gc3_51228.cif" } resolution = 2.46 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= 0.001 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: 5 Type Number sf(0) Gaussians P 80 5.49 5 S 51 5.16 5 C 9358 2.51 5 N 2536 2.21 5 O 3021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15046 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4419 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 11, 'TRANS': 537} Chain breaks: 2 Chain: "B" Number of atoms: 4219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4219 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 514} Chain: "C" Number of atoms: 4768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4768 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 564} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 823 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 817 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Time building chain proxies: 8.76, per 1000 atoms: 0.58 Number of scatterers: 15046 At special positions: 0 Unit cell: (99.462, 131.52, 152.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 80 15.00 O 3021 8.00 N 2536 7.00 C 9358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 25 sheets defined 29.6% alpha, 25.8% beta 40 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 6.65 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.580A pdb=" N GLY A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.749A pdb=" N GLY A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 137 through 147 removed outlier: 4.357A pdb=" N THR A 142 " --> pdb=" O PRO A 138 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLY A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.529A pdb=" N ILE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 Processing helix chain 'A' and resid 352 through 360 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.897A pdb=" N PHE A 545 " --> pdb=" O PHE A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 566 Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 659 through 668 Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.638A pdb=" N GLU B 330 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 592 through 597 Processing helix chain 'C' and resid 51 through 54 Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 323 through 326 removed outlier: 3.519A pdb=" N ASN C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 323 through 326' Processing helix chain 'C' and resid 360 through 363 Processing helix chain 'C' and resid 385 through 394 removed outlier: 3.508A pdb=" N TYR C 389 " --> pdb=" O GLY C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 422 through 432 Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.589A pdb=" N ARG C 437 " --> pdb=" O SER C 433 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 removed outlier: 3.608A pdb=" N TYR C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.588A pdb=" N LEU C 469 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 510 through 514 Processing helix chain 'C' and resid 555 through 558 removed outlier: 3.673A pdb=" N ASP C 558 " --> pdb=" O ILE C 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 555 through 558' Processing helix chain 'C' and resid 564 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 205 removed outlier: 10.568A pdb=" N ASP A 648 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS A 240 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE A 650 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU A 242 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA6, first strand: chain 'A' and resid 569 through 571 Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 140 removed outlier: 6.907A pdb=" N LYS B 139 " --> pdb=" O ASN C 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 238 removed outlier: 6.793A pdb=" N VAL B 234 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B 408 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 343 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 358 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 341 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL B 360 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER B 339 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR B 312 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TRP B 297 " --> pdb=" O TYR B 312 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 314 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE B 295 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 316 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 261 through 265 removed outlier: 6.411A pdb=" N LYS B 255 " --> pdb=" O TYR B 614 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE B 616 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 257 " --> pdb=" O ILE B 616 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 599 " --> pdb=" O ASN B 581 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASN B 581 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ARG B 601 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 579 " --> pdb=" O ARG B 601 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 261 through 265 removed outlier: 6.411A pdb=" N LYS B 255 " --> pdb=" O TYR B 614 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE B 616 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 257 " --> pdb=" O ILE B 616 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 621 " --> pdb=" O ARG B 601 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 272 removed outlier: 4.530A pdb=" N ARG B 282 " --> pdb=" O TYR B 670 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS B 644 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 366 through 371 removed outlier: 5.258A pdb=" N ASP B 368 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 387 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 382 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 425 through 430 removed outlier: 3.533A pdb=" N THR B 427 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 447 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 458 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 467 through 473 removed outlier: 4.386A pdb=" N TYR B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE B 491 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 517 through 520 removed outlier: 6.933A pdb=" N LEU B 535 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 7 through 10 removed outlier: 8.654A pdb=" N SER C 365 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET C 351 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 350 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE C 333 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU C 352 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU C 331 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.904A pdb=" N ILE C 37 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.659A pdb=" N LEU C 103 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS C 91 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 101 " --> pdb=" O CYS C 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 119 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS C 113 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N MET C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 132 through 137 removed outlier: 3.580A pdb=" N CYS C 134 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU C 152 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 153 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER C 173 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE C 155 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.409A pdb=" N VAL C 204 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.561A pdb=" N ASP C 231 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 269 through 272 Processing sheet with id=AC5, first strand: chain 'C' and resid 495 through 499 Processing sheet with id=AC6, first strand: chain 'C' and resid 518 through 520 Processing sheet with id=AC7, first strand: chain 'C' and resid 551 through 553 536 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2298 1.28 - 1.42: 4233 1.42 - 1.56: 8754 1.56 - 1.70: 158 1.70 - 1.84: 79 Bond restraints: 15522 Sorted by residual: bond pdb=" C PRO B 539 " pdb=" O PRO B 539 " ideal model delta sigma weight residual 1.233 1.145 0.089 1.10e-02 8.26e+03 6.50e+01 bond pdb=" C THR B 480 " pdb=" O THR B 480 " ideal model delta sigma weight residual 1.234 1.288 -0.054 1.19e-02 7.06e+03 2.09e+01 bond pdb=" C ILE C 368 " pdb=" O ILE C 368 " ideal model delta sigma weight residual 1.238 1.191 0.047 1.09e-02 8.42e+03 1.85e+01 bond pdb=" C ASP B 636 " pdb=" O ASP B 636 " ideal model delta sigma weight residual 1.234 1.287 -0.053 1.28e-02 6.10e+03 1.69e+01 bond pdb=" C PRO C 88 " pdb=" O PRO C 88 " ideal model delta sigma weight residual 1.233 1.189 0.045 1.10e-02 8.26e+03 1.66e+01 ... (remaining 15517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 19408 2.57 - 5.13: 1822 5.13 - 7.70: 98 7.70 - 10.27: 11 10.27 - 12.84: 2 Bond angle restraints: 21341 Sorted by residual: angle pdb=" CA ASN B 278 " pdb=" CB ASN B 278 " pdb=" CG ASN B 278 " ideal model delta sigma weight residual 112.60 118.77 -6.17 1.00e+00 1.00e+00 3.81e+01 angle pdb=" C4' DG E 17 " pdb=" C3' DG E 17 " pdb=" O3' DG E 17 " ideal model delta sigma weight residual 110.00 100.86 9.14 1.50e+00 4.44e-01 3.71e+01 angle pdb=" CG ARG A 405 " pdb=" CD ARG A 405 " pdb=" NE ARG A 405 " ideal model delta sigma weight residual 112.00 99.16 12.84 2.20e+00 2.07e-01 3.40e+01 angle pdb=" C ALA C 24 " pdb=" N ARG C 25 " pdb=" CA ARG C 25 " ideal model delta sigma weight residual 120.38 128.36 -7.98 1.37e+00 5.33e-01 3.39e+01 angle pdb=" N MET B 331 " pdb=" CA MET B 331 " pdb=" CB MET B 331 " ideal model delta sigma weight residual 110.20 101.53 8.67 1.49e+00 4.50e-01 3.39e+01 ... (remaining 21336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 8588 34.04 - 68.08: 538 68.08 - 102.12: 9 102.12 - 136.16: 0 136.16 - 170.20: 1 Dihedral angle restraints: 9136 sinusoidal: 4218 harmonic: 4918 Sorted by residual: dihedral pdb=" CA MET B 141 " pdb=" C MET B 141 " pdb=" N LYS B 142 " pdb=" CA LYS B 142 " ideal model delta harmonic sigma weight residual 180.00 -146.37 -33.63 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA ILE C 463 " pdb=" C ILE C 463 " pdb=" N ASN C 464 " pdb=" CA ASN C 464 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU C 73 " pdb=" C LEU C 73 " pdb=" N ALA C 74 " pdb=" CA ALA C 74 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 9133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2070 0.128 - 0.257: 271 0.257 - 0.385: 40 0.385 - 0.513: 34 0.513 - 0.642: 3 Chirality restraints: 2418 Sorted by residual: chirality pdb=" P DG D 46 " pdb=" OP1 DG D 46 " pdb=" OP2 DG D 46 " pdb=" O5' DG D 46 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DA E 1 " pdb=" OP1 DA E 1 " pdb=" OP2 DA E 1 " pdb=" O5' DA E 1 " both_signs ideal model delta sigma weight residual True 2.35 2.94 -0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" P DA D 54 " pdb=" OP1 DA D 54 " pdb=" OP2 DA D 54 " pdb=" O5' DA D 54 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.29e+00 ... (remaining 2415 not shown) Planarity restraints: 2417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 526 " 0.082 2.00e-02 2.50e+03 4.73e-02 4.47e+01 pdb=" CG TYR B 526 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 526 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR B 526 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR B 526 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 526 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 526 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 65 " -0.047 2.00e-02 2.50e+03 2.86e-02 2.46e+01 pdb=" N9 DG D 65 " 0.005 2.00e-02 2.50e+03 pdb=" C8 DG D 65 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG D 65 " 0.037 2.00e-02 2.50e+03 pdb=" C5 DG D 65 " 0.024 2.00e-02 2.50e+03 pdb=" C6 DG D 65 " -0.019 2.00e-02 2.50e+03 pdb=" O6 DG D 65 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG D 65 " -0.051 2.00e-02 2.50e+03 pdb=" C2 DG D 65 " -0.011 2.00e-02 2.50e+03 pdb=" N2 DG D 65 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DG D 65 " 0.043 2.00e-02 2.50e+03 pdb=" C4 DG D 65 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 297 " -0.063 2.00e-02 2.50e+03 3.00e-02 2.25e+01 pdb=" CG TRP B 297 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 297 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 297 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 297 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 297 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 297 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 297 " -0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 297 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP B 297 " -0.015 2.00e-02 2.50e+03 ... (remaining 2414 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3526 2.83 - 3.35: 13659 3.35 - 3.86: 25822 3.86 - 4.38: 32327 4.38 - 4.90: 51337 Nonbonded interactions: 126671 Sorted by model distance: nonbonded pdb=" OH TYR A 258 " pdb=" OD1 ASP A 261 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 395 " pdb=" OP1 DT D 68 " model vdw 2.324 3.040 nonbonded pdb=" NH1 ARG A 204 " pdb=" OE1 GLU A 212 " model vdw 2.357 3.120 nonbonded pdb=" OG SER C 339 " pdb=" OD1 ASP C 341 " model vdw 2.360 3.040 nonbonded pdb=" OH TYR B 607 " pdb=" OD1 ASP B 612 " model vdw 2.369 3.040 ... (remaining 126666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 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: 1.890 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 40.990 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 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 : 0.013 0.089 15522 Z= 0.842 Angle : 1.539 12.836 21341 Z= 1.031 Chirality : 0.107 0.642 2418 Planarity : 0.009 0.125 2417 Dihedral : 18.376 170.197 5954 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.68 (0.19), residues: 1663 helix: -0.97 (0.23), residues: 397 sheet: 0.12 (0.23), residues: 429 loop : -0.36 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.012 TRP B 297 HIS 0.012 0.003 HIS A 162 PHE 0.043 0.009 PHE A 404 TYR 0.082 0.009 TYR B 526 ARG 0.039 0.003 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.608 Fit side-chains REVERT: A 81 HIS cc_start: 0.8831 (m90) cc_final: 0.8575 (m90) REVERT: A 132 GLN cc_start: 0.9264 (tt0) cc_final: 0.8962 (tm-30) REVERT: A 575 GLN cc_start: 0.8917 (tt0) cc_final: 0.8703 (pp30) REVERT: A 629 ASP cc_start: 0.9596 (m-30) cc_final: 0.9334 (p0) REVERT: B 152 GLN cc_start: 0.8749 (mt0) cc_final: 0.8338 (mm110) REVERT: B 331 MET cc_start: 0.9162 (ttt) cc_final: 0.8953 (ttt) REVERT: C 296 ASP cc_start: 0.9064 (m-30) cc_final: 0.8862 (p0) REVERT: C 299 HIS cc_start: 0.8867 (t70) cc_final: 0.8412 (m-70) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 1.5929 time to fit residues: 217.4160 Evaluate side-chains 70 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 72 optimal weight: 0.0170 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 82 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 450 ASN B 204 GLN C 41 GLN C 76 GLN C 106 ASN C 364 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15522 Z= 0.167 Angle : 0.557 8.150 21341 Z= 0.318 Chirality : 0.041 0.163 2418 Planarity : 0.003 0.036 2417 Dihedral : 20.532 178.477 2680 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.53 % Allowed : 4.76 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.44 (0.20), residues: 1663 helix: 0.82 (0.26), residues: 406 sheet: 0.24 (0.23), residues: 462 loop : 0.21 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 647 HIS 0.004 0.001 HIS B 236 PHE 0.014 0.001 PHE C 441 TYR 0.015 0.001 TYR B 235 ARG 0.004 0.000 ARG A 596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9195 (tt0) cc_final: 0.8975 (tm-30) REVERT: B 152 GLN cc_start: 0.8749 (mt0) cc_final: 0.8393 (mm110) REVERT: C 296 ASP cc_start: 0.9104 (m-30) cc_final: 0.8867 (p0) REVERT: C 432 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9056 (mmtp) REVERT: C 502 PHE cc_start: 0.8295 (m-80) cc_final: 0.7969 (m-80) outliers start: 8 outliers final: 3 residues processed: 84 average time/residue: 1.5413 time to fit residues: 143.1653 Evaluate side-chains 61 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 432 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN B 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15522 Z= 0.302 Angle : 0.574 7.659 21341 Z= 0.322 Chirality : 0.043 0.214 2418 Planarity : 0.004 0.065 2417 Dihedral : 20.608 178.754 2680 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.93 % Allowed : 6.28 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.53 (0.20), residues: 1663 helix: 1.07 (0.26), residues: 405 sheet: 0.22 (0.23), residues: 451 loop : 0.20 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 231 HIS 0.004 0.001 HIS B 236 PHE 0.015 0.002 PHE B 200 TYR 0.016 0.001 TYR B 235 ARG 0.005 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9189 (tt0) cc_final: 0.8905 (tm-30) REVERT: A 612 THR cc_start: 0.9415 (m) cc_final: 0.9150 (t) REVERT: B 141 MET cc_start: 0.4735 (ptm) cc_final: 0.4362 (mtp) REVERT: B 152 GLN cc_start: 0.8774 (mt0) cc_final: 0.8440 (mm110) REVERT: C 296 ASP cc_start: 0.9144 (m-30) cc_final: 0.8896 (p0) REVERT: C 432 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9036 (mmtm) outliers start: 14 outliers final: 6 residues processed: 78 average time/residue: 1.4746 time to fit residues: 127.3762 Evaluate side-chains 65 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 432 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15522 Z= 0.395 Angle : 0.595 6.344 21341 Z= 0.331 Chirality : 0.045 0.237 2418 Planarity : 0.004 0.068 2417 Dihedral : 20.475 177.432 2680 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.39 % Allowed : 6.94 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.45 (0.20), residues: 1663 helix: 1.16 (0.26), residues: 402 sheet: 0.16 (0.23), residues: 451 loop : 0.08 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 231 HIS 0.007 0.001 HIS B 236 PHE 0.016 0.002 PHE B 200 TYR 0.016 0.002 TYR B 235 ARG 0.007 0.001 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9225 (tt0) cc_final: 0.8961 (tm-30) REVERT: A 612 THR cc_start: 0.9463 (m) cc_final: 0.9228 (t) REVERT: B 141 MET cc_start: 0.4732 (ptm) cc_final: 0.4390 (mtp) REVERT: B 152 GLN cc_start: 0.8792 (mt0) cc_final: 0.8449 (mm110) REVERT: C 296 ASP cc_start: 0.9110 (m-30) cc_final: 0.8876 (p0) REVERT: C 432 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9055 (mmtm) outliers start: 21 outliers final: 11 residues processed: 80 average time/residue: 1.4452 time to fit residues: 128.0433 Evaluate side-chains 71 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.9081 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15522 Z= 0.169 Angle : 0.501 8.077 21341 Z= 0.283 Chirality : 0.041 0.144 2418 Planarity : 0.003 0.037 2417 Dihedral : 20.000 179.492 2680 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.86 % Allowed : 7.87 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.61 (0.20), residues: 1663 helix: 1.37 (0.26), residues: 409 sheet: 0.15 (0.23), residues: 466 loop : 0.19 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 231 HIS 0.004 0.001 HIS A 188 PHE 0.015 0.001 PHE C 441 TYR 0.012 0.001 TYR B 235 ARG 0.006 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9215 (tt0) cc_final: 0.8971 (tm-30) REVERT: A 596 ARG cc_start: 0.9041 (tpt-90) cc_final: 0.8787 (mmm160) REVERT: A 612 THR cc_start: 0.9423 (m) cc_final: 0.9180 (t) REVERT: B 141 MET cc_start: 0.4704 (ptm) cc_final: 0.4356 (mtp) REVERT: B 152 GLN cc_start: 0.8728 (mt0) cc_final: 0.8409 (mm110) REVERT: C 296 ASP cc_start: 0.9122 (m-30) cc_final: 0.8870 (p0) REVERT: C 351 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8148 (mtt) REVERT: C 432 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9035 (mmtm) REVERT: C 502 PHE cc_start: 0.8130 (m-80) cc_final: 0.7816 (m-80) outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 1.3321 time to fit residues: 103.0151 Evaluate side-chains 69 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.9118 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15522 Z= 0.281 Angle : 0.540 9.337 21341 Z= 0.300 Chirality : 0.042 0.185 2418 Planarity : 0.003 0.055 2417 Dihedral : 20.173 177.364 2680 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.19 % Allowed : 7.74 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.60 (0.20), residues: 1663 helix: 1.38 (0.26), residues: 409 sheet: 0.17 (0.23), residues: 461 loop : 0.16 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 231 HIS 0.005 0.001 HIS B 236 PHE 0.014 0.001 PHE C 441 TYR 0.013 0.001 TYR B 235 ARG 0.005 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9233 (tt0) cc_final: 0.8968 (tm-30) REVERT: A 596 ARG cc_start: 0.9041 (tpt-90) cc_final: 0.8780 (mmm160) REVERT: A 612 THR cc_start: 0.9439 (m) cc_final: 0.9209 (t) REVERT: B 141 MET cc_start: 0.4720 (ptm) cc_final: 0.4371 (mtp) REVERT: B 152 GLN cc_start: 0.8755 (mt0) cc_final: 0.8431 (mm110) REVERT: C 296 ASP cc_start: 0.9119 (m-30) cc_final: 0.8867 (p0) REVERT: C 351 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8271 (mtt) REVERT: C 432 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9031 (mmtp) outliers start: 18 outliers final: 10 residues processed: 75 average time/residue: 1.3358 time to fit residues: 111.9926 Evaluate side-chains 71 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 95 optimal weight: 0.0870 chunk 122 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15522 Z= 0.144 Angle : 0.484 9.611 21341 Z= 0.270 Chirality : 0.040 0.136 2418 Planarity : 0.003 0.033 2417 Dihedral : 19.731 178.913 2680 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.99 % Allowed : 8.27 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.76 (0.21), residues: 1663 helix: 1.59 (0.26), residues: 409 sheet: 0.23 (0.23), residues: 453 loop : 0.23 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 231 HIS 0.003 0.001 HIS B 236 PHE 0.014 0.001 PHE C 441 TYR 0.012 0.001 TYR B 235 ARG 0.005 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9205 (tt0) cc_final: 0.8952 (tm-30) REVERT: A 198 ARG cc_start: 0.9208 (tpp-160) cc_final: 0.8375 (tmm160) REVERT: A 596 ARG cc_start: 0.9016 (tpt-90) cc_final: 0.8782 (mmm160) REVERT: A 612 THR cc_start: 0.9362 (m) cc_final: 0.9121 (t) REVERT: B 141 MET cc_start: 0.4591 (ptm) cc_final: 0.4239 (mtp) REVERT: B 152 GLN cc_start: 0.8829 (mt0) cc_final: 0.8545 (mm110) REVERT: C 296 ASP cc_start: 0.9087 (m-30) cc_final: 0.8836 (p0) REVERT: C 351 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8067 (mtt) REVERT: C 432 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9059 (mmtm) REVERT: C 502 PHE cc_start: 0.7809 (m-80) cc_final: 0.7331 (m-80) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 1.3696 time to fit residues: 122.3852 Evaluate side-chains 73 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15522 Z= 0.164 Angle : 0.501 10.830 21341 Z= 0.275 Chirality : 0.040 0.138 2418 Planarity : 0.003 0.036 2417 Dihedral : 19.786 177.432 2680 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.73 % Allowed : 8.60 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.79 (0.21), residues: 1663 helix: 1.66 (0.26), residues: 408 sheet: 0.25 (0.23), residues: 453 loop : 0.23 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 PHE 0.013 0.001 PHE C 441 TYR 0.012 0.001 TYR B 235 ARG 0.006 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9207 (tt0) cc_final: 0.8949 (tm-30) REVERT: A 198 ARG cc_start: 0.9209 (tpp-160) cc_final: 0.8414 (tmm160) REVERT: A 596 ARG cc_start: 0.9027 (tpt-90) cc_final: 0.8791 (mmm160) REVERT: A 612 THR cc_start: 0.9353 (m) cc_final: 0.9110 (t) REVERT: B 141 MET cc_start: 0.4587 (ptm) cc_final: 0.4237 (mtp) REVERT: B 152 GLN cc_start: 0.8892 (mt0) cc_final: 0.8617 (mm110) REVERT: C 296 ASP cc_start: 0.9092 (m-30) cc_final: 0.8838 (p0) REVERT: C 351 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8121 (mtt) REVERT: C 432 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9050 (mmtm) REVERT: C 502 PHE cc_start: 0.7840 (m-80) cc_final: 0.7404 (m-80) outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 1.4590 time to fit residues: 112.4795 Evaluate side-chains 72 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 6.9990 chunk 145 optimal weight: 0.2980 chunk 155 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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: 0.9090 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15522 Z= 0.212 Angle : 0.519 11.480 21341 Z= 0.284 Chirality : 0.041 0.151 2418 Planarity : 0.003 0.044 2417 Dihedral : 19.863 176.232 2680 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.86 % Allowed : 8.66 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.77 (0.21), residues: 1663 helix: 1.63 (0.26), residues: 408 sheet: 0.22 (0.23), residues: 456 loop : 0.23 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 PHE 0.013 0.001 PHE C 441 TYR 0.012 0.001 TYR B 235 ARG 0.006 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9208 (tt0) cc_final: 0.8945 (tm-30) REVERT: A 198 ARG cc_start: 0.9209 (tpp-160) cc_final: 0.8426 (tmm160) REVERT: A 596 ARG cc_start: 0.9034 (tpt-90) cc_final: 0.8793 (mmm160) REVERT: A 612 THR cc_start: 0.9347 (m) cc_final: 0.9114 (t) REVERT: B 141 MET cc_start: 0.4540 (ptm) cc_final: 0.4211 (mtp) REVERT: B 152 GLN cc_start: 0.8825 (mt0) cc_final: 0.8542 (mm110) REVERT: C 296 ASP cc_start: 0.9089 (m-30) cc_final: 0.8830 (p0) REVERT: C 351 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8177 (mtt) REVERT: C 432 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9041 (mmtp) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 1.3644 time to fit residues: 109.5901 Evaluate side-chains 71 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 158 optimal weight: 0.1980 chunk 137 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.9079 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15522 Z= 0.188 Angle : 0.506 12.050 21341 Z= 0.278 Chirality : 0.040 0.139 2418 Planarity : 0.003 0.038 2417 Dihedral : 19.777 176.112 2680 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.73 % Allowed : 8.66 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.78 (0.21), residues: 1663 helix: 1.66 (0.26), residues: 408 sheet: 0.22 (0.24), residues: 453 loop : 0.23 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 PHE 0.014 0.001 PHE C 441 TYR 0.012 0.001 TYR B 235 ARG 0.006 0.000 ARG B 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.9199 (tt0) cc_final: 0.8931 (tm-30) REVERT: A 198 ARG cc_start: 0.9205 (tpp-160) cc_final: 0.8435 (tmm160) REVERT: A 596 ARG cc_start: 0.9028 (tpt-90) cc_final: 0.8787 (mmm160) REVERT: A 612 THR cc_start: 0.9336 (m) cc_final: 0.9107 (t) REVERT: B 141 MET cc_start: 0.4524 (ptm) cc_final: 0.4191 (mtp) REVERT: B 152 GLN cc_start: 0.8893 (mt0) cc_final: 0.8617 (mm110) REVERT: C 296 ASP cc_start: 0.9088 (m-30) cc_final: 0.8835 (p0) REVERT: C 351 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8156 (mtt) REVERT: C 432 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9096 (mmtm) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 1.4494 time to fit residues: 115.8281 Evaluate side-chains 73 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain C residue 299 HIS Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.2980 chunk 42 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 20 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 25 optimal weight: 30.0000 chunk 120 optimal weight: 1.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.090750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.061456 restraints weight = 30808.523| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.55 r_work: 0.2898 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15522 Z= 0.126 Angle : 0.475 9.432 21341 Z= 0.262 Chirality : 0.039 0.136 2418 Planarity : 0.003 0.033 2417 Dihedral : 19.447 176.445 2680 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.53 % Allowed : 8.86 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.90 (0.21), residues: 1663 helix: 1.85 (0.27), residues: 407 sheet: 0.30 (0.23), residues: 452 loop : 0.24 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 231 HIS 0.004 0.000 HIS B 236 PHE 0.029 0.001 PHE C 502 TYR 0.012 0.001 TYR B 235 ARG 0.006 0.000 ARG B 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3926.78 seconds wall clock time: 72 minutes 24.47 seconds (4344.47 seconds total)