Starting phenix.real_space_refine on Fri Jun 13 12:30:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gc3_51228/06_2025/9gc3_51228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gc3_51228/06_2025/9gc3_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_51228/06_2025/9gc3_51228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gc3_51228/06_2025/9gc3_51228.map" model { file = "/net/cci-nas-00/data/ceres_data/9gc3_51228/06_2025/9gc3_51228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gc3_51228/06_2025/9gc3_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-5710/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: 8.78, 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: 3.50 Conformation dependent library (CDL) restraints added in 1.7 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: 5.87 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: 7.24 Time building geometry restraints manager: 4.20 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: 2.100 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.010 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.860 ------------------------------------------------------------------------------- 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= 0.934 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 Details of bonding type rmsd hydrogen bonds : bond 0.17778 ( 623) hydrogen bonds : angle 7.30813 ( 1659) covalent geometry : bond 0.01332 (15522) covalent geometry : angle 1.53866 (21341) *********************** 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 : 1.825 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: 1.6671 time to fit residues: 227.8896 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 : 1.781 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.090205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059994 restraints weight = 30183.756| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.64 r_work: 0.2855 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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= 0.128 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 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 623) hydrogen bonds : angle 4.86954 ( 1659) covalent geometry : bond 0.00279 (15522) covalent geometry : angle 0.55681 (21341) *********************** 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 : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8874 (tt0) cc_final: 0.8651 (tm-30) REVERT: B 152 GLN cc_start: 0.8255 (mt0) cc_final: 0.7933 (mm110) REVERT: B 253 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8494 (mtp85) REVERT: C 116 LYS cc_start: 0.8711 (tppp) cc_final: 0.8495 (ttpt) REVERT: C 126 ASN cc_start: 0.7631 (p0) cc_final: 0.7258 (p0) REVERT: C 432 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8587 (mmtp) REVERT: C 502 PHE cc_start: 0.8045 (m-80) cc_final: 0.7650 (m-80) outliers start: 8 outliers final: 3 residues processed: 84 average time/residue: 1.8662 time to fit residues: 172.4393 Evaluate side-chains 63 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 2.577 ------------------------------------------------------------------------------- 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 104 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN B 372 HIS C 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.055563 restraints weight = 30013.433| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.62 r_work: 0.2751 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15522 Z= 0.272 Angle : 0.615 8.390 21341 Z= 0.343 Chirality : 0.045 0.260 2418 Planarity : 0.004 0.069 2417 Dihedral : 20.777 177.987 2680 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.12 % Allowed : 6.28 % Favored : 92.59 % 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: 0.43 (0.20), residues: 1663 helix: 0.97 (0.26), residues: 405 sheet: 0.18 (0.23), residues: 451 loop : 0.14 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 231 HIS 0.005 0.001 HIS B 236 PHE 0.016 0.002 PHE B 200 TYR 0.017 0.002 TYR B 235 ARG 0.006 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 623) hydrogen bonds : angle 4.89185 ( 1659) covalent geometry : bond 0.00635 (15522) covalent geometry : angle 0.61546 (21341) *********************** 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 85 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 1.637 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8847 (tt0) cc_final: 0.8549 (tm-30) REVERT: A 435 ARG cc_start: 0.8333 (mmt-90) cc_final: 0.8050 (mmp80) REVERT: A 612 THR cc_start: 0.9331 (m) cc_final: 0.9047 (t) REVERT: A 633 ARG cc_start: 0.8842 (ptp90) cc_final: 0.8633 (ttp80) REVERT: B 141 MET cc_start: 0.4662 (ptm) cc_final: 0.4204 (mtp) REVERT: B 152 GLN cc_start: 0.8277 (mt0) cc_final: 0.8000 (mm110) REVERT: C 116 LYS cc_start: 0.8642 (tppp) cc_final: 0.8423 (ttpt) REVERT: C 432 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8514 (mmtm) outliers start: 17 outliers final: 8 residues processed: 80 average time/residue: 1.4160 time to fit residues: 125.2404 Evaluate side-chains 68 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 300 ILE 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 408 MET 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 44 optimal weight: 0.5980 chunk 171 optimal weight: 3.9990 chunk 161 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 169 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 overall best weight: 0.3014 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.090110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.060520 restraints weight = 30286.778| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.57 r_work: 0.2888 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2936 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= 0.102 Angle : 0.487 7.185 21341 Z= 0.276 Chirality : 0.040 0.147 2418 Planarity : 0.003 0.034 2417 Dihedral : 19.846 177.750 2680 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % 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: 0.63 (0.20), residues: 1663 helix: 1.39 (0.26), residues: 403 sheet: 0.15 (0.23), residues: 461 loop : 0.22 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 231 HIS 0.003 0.000 HIS B 236 PHE 0.015 0.001 PHE C 441 TYR 0.012 0.001 TYR B 235 ARG 0.009 0.000 ARG A 573 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 623) hydrogen bonds : angle 4.42131 ( 1659) covalent geometry : bond 0.00217 (15522) covalent geometry : angle 0.48667 (21341) *********************** 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 77 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8796 (tt0) cc_final: 0.8508 (tm-30) REVERT: A 596 ARG cc_start: 0.8548 (tpt-90) cc_final: 0.8170 (mmm160) REVERT: A 612 THR cc_start: 0.9254 (m) cc_final: 0.8946 (t) REVERT: A 633 ARG cc_start: 0.8880 (ptp90) cc_final: 0.8514 (ptp-170) REVERT: B 141 MET cc_start: 0.4138 (ptm) cc_final: 0.3783 (mtp) REVERT: B 152 GLN cc_start: 0.8336 (mt0) cc_final: 0.8121 (mm110) REVERT: B 253 ARG cc_start: 0.8746 (mtp85) cc_final: 0.8308 (mtm180) REVERT: C 432 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8577 (mmtm) REVERT: C 502 PHE cc_start: 0.7905 (m-80) cc_final: 0.7527 (m-80) outliers start: 12 outliers final: 4 residues processed: 73 average time/residue: 1.4239 time to fit residues: 115.2775 Evaluate side-chains 65 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 348 VAL Chi-restraints excluded: chain C residue 432 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 74 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.088129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057874 restraints weight = 30647.426| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.57 r_work: 0.2816 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2903 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= 0.145 Angle : 0.508 9.589 21341 Z= 0.284 Chirality : 0.041 0.151 2418 Planarity : 0.003 0.046 2417 Dihedral : 20.039 178.850 2680 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.93 % Allowed : 7.54 % Favored : 91.53 % 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: 0.71 (0.20), residues: 1663 helix: 1.47 (0.26), residues: 407 sheet: 0.17 (0.23), residues: 461 loop : 0.28 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 PHE 0.012 0.001 PHE C 441 TYR 0.013 0.001 TYR B 235 ARG 0.004 0.000 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 623) hydrogen bonds : angle 4.44619 ( 1659) covalent geometry : bond 0.00330 (15522) covalent geometry : angle 0.50822 (21341) *********************** 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 77 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8848 (tt0) cc_final: 0.8559 (tm-30) REVERT: A 612 THR cc_start: 0.9264 (m) cc_final: 0.8969 (t) REVERT: B 141 MET cc_start: 0.4207 (ptm) cc_final: 0.3843 (mtp) REVERT: B 152 GLN cc_start: 0.8365 (mt0) cc_final: 0.8145 (mm110) REVERT: B 253 ARG cc_start: 0.8735 (mtp85) cc_final: 0.8434 (mtm180) REVERT: C 126 ASN cc_start: 0.8077 (p0) cc_final: 0.7751 (p0) REVERT: C 351 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: C 432 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8599 (mmtm) REVERT: C 502 PHE cc_start: 0.7900 (m-80) cc_final: 0.7588 (m-80) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 1.3005 time to fit residues: 104.9211 Evaluate side-chains 71 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 369 MET Chi-restraints excluded: chain C residue 432 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 163 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 115 optimal weight: 0.0980 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.087000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056540 restraints weight = 30354.821| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.57 r_work: 0.2769 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15522 Z= 0.195 Angle : 0.542 10.400 21341 Z= 0.300 Chirality : 0.042 0.183 2418 Planarity : 0.003 0.054 2417 Dihedral : 20.135 177.420 2680 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.79 % Allowed : 8.00 % Favored : 91.20 % 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: 0.66 (0.20), residues: 1663 helix: 1.41 (0.26), residues: 409 sheet: 0.17 (0.23), residues: 450 loop : 0.23 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 231 HIS 0.005 0.001 HIS B 236 PHE 0.013 0.001 PHE B 200 TYR 0.013 0.001 TYR B 235 ARG 0.006 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 623) hydrogen bonds : angle 4.54658 ( 1659) covalent geometry : bond 0.00452 (15522) covalent geometry : angle 0.54186 (21341) *********************** 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 76 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.787 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5485 (tmt) cc_final: 0.5190 (tmt) REVERT: A 132 GLN cc_start: 0.8882 (tt0) cc_final: 0.8641 (tm-30) REVERT: A 612 THR cc_start: 0.9292 (m) cc_final: 0.9023 (t) REVERT: A 633 ARG cc_start: 0.8887 (ptp90) cc_final: 0.8643 (ptp-110) REVERT: B 141 MET cc_start: 0.4199 (ptm) cc_final: 0.3829 (mtp) REVERT: B 152 GLN cc_start: 0.8263 (mt0) cc_final: 0.7999 (mm110) REVERT: B 253 ARG cc_start: 0.8739 (mtp85) cc_final: 0.8411 (mtm180) REVERT: C 126 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7902 (p0) REVERT: C 174 ILE cc_start: 0.9003 (mt) cc_final: 0.8734 (tt) REVERT: C 351 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8021 (mtt) REVERT: C 432 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8557 (mmtp) REVERT: C 497 LEU cc_start: 0.9133 (tp) cc_final: 0.8881 (tm) REVERT: C 502 PHE cc_start: 0.7972 (m-80) cc_final: 0.7682 (m-80) outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 1.3508 time to fit residues: 107.6920 Evaluate side-chains 74 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 126 ASN 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 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 63 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.088554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058308 restraints weight = 30493.951| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.57 r_work: 0.2829 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3108 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= 0.137 Angle : 0.502 11.047 21341 Z= 0.279 Chirality : 0.040 0.141 2418 Planarity : 0.003 0.039 2417 Dihedral : 19.863 178.170 2680 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.93 % Allowed : 7.94 % Favored : 91.14 % 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: 0.75 (0.21), residues: 1663 helix: 1.51 (0.26), residues: 409 sheet: 0.20 (0.23), residues: 453 loop : 0.28 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 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 0.005 0.000 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 623) hydrogen bonds : angle 4.40299 ( 1659) covalent geometry : bond 0.00312 (15522) covalent geometry : angle 0.50201 (21341) *********************** 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 81 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 1.756 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5534 (tmt) cc_final: 0.5099 (tmt) REVERT: A 132 GLN cc_start: 0.8824 (tt0) cc_final: 0.8584 (tm-30) REVERT: A 596 ARG cc_start: 0.8548 (tpt-90) cc_final: 0.8114 (mmm160) REVERT: A 612 THR cc_start: 0.9253 (m) cc_final: 0.8987 (t) REVERT: A 633 ARG cc_start: 0.8898 (ptp90) cc_final: 0.8644 (ptp-110) REVERT: B 141 MET cc_start: 0.4144 (ptm) cc_final: 0.3768 (mtp) REVERT: B 152 GLN cc_start: 0.8314 (mt0) cc_final: 0.8088 (mm110) REVERT: B 253 ARG cc_start: 0.8792 (mtp85) cc_final: 0.8507 (mtm180) REVERT: C 126 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7734 (p0) REVERT: C 174 ILE cc_start: 0.8954 (mt) cc_final: 0.8715 (tt) REVERT: C 351 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7937 (mtt) REVERT: C 432 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8561 (mmtp) REVERT: C 497 LEU cc_start: 0.9136 (tp) cc_final: 0.8890 (tm) REVERT: C 502 PHE cc_start: 0.7877 (m-80) cc_final: 0.7533 (m-80) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 1.3806 time to fit residues: 115.1786 Evaluate side-chains 78 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 126 ASN 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 369 MET Chi-restraints excluded: chain C residue 432 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 4 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.088121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058102 restraints weight = 30330.824| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.55 r_work: 0.2814 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15522 Z= 0.140 Angle : 0.509 11.860 21341 Z= 0.281 Chirality : 0.041 0.143 2418 Planarity : 0.003 0.043 2417 Dihedral : 19.872 177.077 2680 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.99 % Allowed : 8.00 % Favored : 91.01 % 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: 1.54 (0.26), residues: 408 sheet: 0.17 (0.24), residues: 447 loop : 0.30 (0.22), residues: 808 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 0.004 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 623) hydrogen bonds : angle 4.38989 ( 1659) covalent geometry : bond 0.00321 (15522) covalent geometry : angle 0.50863 (21341) *********************** 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 81 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5308 (tmt) cc_final: 0.4588 (tmt) REVERT: A 132 GLN cc_start: 0.8862 (tt0) cc_final: 0.8609 (tm-30) REVERT: A 198 ARG cc_start: 0.9229 (tpp-160) cc_final: 0.8140 (tmm160) REVERT: A 596 ARG cc_start: 0.8605 (tpt-90) cc_final: 0.8180 (mmm160) REVERT: A 612 THR cc_start: 0.9230 (m) cc_final: 0.8969 (t) REVERT: A 633 ARG cc_start: 0.8920 (ptp90) cc_final: 0.8699 (ptp-110) REVERT: B 141 MET cc_start: 0.4179 (ptm) cc_final: 0.3801 (mtp) REVERT: B 152 GLN cc_start: 0.8390 (mt0) cc_final: 0.8164 (mm110) REVERT: B 253 ARG cc_start: 0.8815 (mtp85) cc_final: 0.8537 (mtm180) REVERT: C 100 MET cc_start: 0.9356 (ptt) cc_final: 0.9086 (ptt) REVERT: C 126 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7834 (p0) REVERT: C 174 ILE cc_start: 0.8993 (mt) cc_final: 0.8749 (tt) REVERT: C 351 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7959 (mtt) REVERT: C 432 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8639 (mmtm) REVERT: C 497 LEU cc_start: 0.9128 (tp) cc_final: 0.8879 (tm) REVERT: C 502 PHE cc_start: 0.7862 (m-80) cc_final: 0.7620 (m-80) outliers start: 15 outliers final: 10 residues processed: 74 average time/residue: 1.4082 time to fit residues: 115.7110 Evaluate side-chains 79 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 415 SER Chi-restraints excluded: chain C residue 126 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 153 optimal weight: 0.0980 chunk 140 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 28 optimal weight: 0.0270 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.089975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060226 restraints weight = 30692.692| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.59 r_work: 0.2864 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15522 Z= 0.100 Angle : 0.480 11.938 21341 Z= 0.265 Chirality : 0.040 0.135 2418 Planarity : 0.003 0.033 2417 Dihedral : 19.579 177.523 2680 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.73 % Allowed : 8.33 % Favored : 90.94 % 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: 0.85 (0.21), residues: 1663 helix: 1.70 (0.26), residues: 407 sheet: 0.19 (0.24), residues: 444 loop : 0.33 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 231 HIS 0.003 0.000 HIS B 236 PHE 0.013 0.001 PHE C 441 TYR 0.011 0.001 TYR B 235 ARG 0.003 0.000 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 623) hydrogen bonds : angle 4.23382 ( 1659) covalent geometry : bond 0.00219 (15522) covalent geometry : angle 0.47988 (21341) *********************** 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 81 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8799 (tt0) cc_final: 0.8541 (tm-30) REVERT: A 198 ARG cc_start: 0.9233 (tpp-160) cc_final: 0.8164 (tmm160) REVERT: A 561 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7686 (mppt) REVERT: A 596 ARG cc_start: 0.8529 (tpt-90) cc_final: 0.8170 (mmm160) REVERT: A 612 THR cc_start: 0.9178 (m) cc_final: 0.8919 (t) REVERT: B 141 MET cc_start: 0.4023 (ptm) cc_final: 0.3643 (mtp) REVERT: B 152 GLN cc_start: 0.8386 (mt0) cc_final: 0.8177 (mm110) REVERT: B 253 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8592 (mtp85) REVERT: C 100 MET cc_start: 0.9301 (ptt) cc_final: 0.9048 (ptt) REVERT: C 126 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7693 (p0) REVERT: C 351 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: C 432 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8647 (mmtm) REVERT: C 497 LEU cc_start: 0.9146 (tp) cc_final: 0.8917 (tm) REVERT: C 502 PHE cc_start: 0.7757 (m-80) cc_final: 0.7431 (m-80) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 1.3891 time to fit residues: 118.7751 Evaluate side-chains 73 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 126 ASN 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 369 MET Chi-restraints excluded: chain C residue 432 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 141 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 71 optimal weight: 0.0470 chunk 118 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.089429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059576 restraints weight = 30708.903| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.59 r_work: 0.2848 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3441 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= 0.111 Angle : 0.486 12.333 21341 Z= 0.268 Chirality : 0.040 0.139 2418 Planarity : 0.003 0.034 2417 Dihedral : 19.615 176.471 2680 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.66 % Allowed : 8.53 % Favored : 90.81 % 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: 0.85 (0.21), residues: 1663 helix: 1.69 (0.26), residues: 408 sheet: 0.26 (0.23), residues: 454 loop : 0.29 (0.22), residues: 801 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 0.013 0.001 PHE C 441 TYR 0.012 0.001 TYR B 235 ARG 0.004 0.000 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.02968 ( 623) hydrogen bonds : angle 4.23278 ( 1659) covalent geometry : bond 0.00248 (15522) covalent geometry : angle 0.48570 (21341) ********************** 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 74 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8814 (tt0) cc_final: 0.8542 (tm-30) REVERT: A 198 ARG cc_start: 0.9229 (tpp-160) cc_final: 0.8178 (tmm160) REVERT: A 596 ARG cc_start: 0.8551 (tpt-90) cc_final: 0.8186 (mmm160) REVERT: A 612 THR cc_start: 0.9167 (m) cc_final: 0.8910 (t) REVERT: B 141 MET cc_start: 0.4079 (ptm) cc_final: 0.3711 (mtp) REVERT: B 152 GLN cc_start: 0.8425 (mt0) cc_final: 0.8215 (mm110) REVERT: B 253 ARG cc_start: 0.8838 (mtp85) cc_final: 0.8596 (mtp85) REVERT: C 126 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7703 (p0) REVERT: C 351 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7867 (mtt) REVERT: C 431 MET cc_start: 0.8815 (mmm) cc_final: 0.8559 (mmm) REVERT: C 432 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8624 (mmtm) REVERT: C 497 LEU cc_start: 0.9149 (tp) cc_final: 0.8921 (tm) REVERT: C 502 PHE cc_start: 0.7771 (m-80) cc_final: 0.7454 (m-80) outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 1.3226 time to fit residues: 101.7202 Evaluate side-chains 71 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 126 ASN 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 369 MET Chi-restraints excluded: chain C residue 432 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 132 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.088528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058844 restraints weight = 30419.373| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.51 r_work: 0.2829 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15522 Z= 0.132 Angle : 0.497 12.333 21341 Z= 0.274 Chirality : 0.040 0.141 2418 Planarity : 0.003 0.040 2417 Dihedral : 19.693 175.585 2680 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.79 % Allowed : 8.53 % 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: 0.84 (0.21), residues: 1663 helix: 1.67 (0.26), residues: 408 sheet: 0.27 (0.24), residues: 453 loop : 0.28 (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 0.013 0.001 PHE C 441 TYR 0.013 0.001 TYR B 235 ARG 0.004 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 623) hydrogen bonds : angle 4.30442 ( 1659) covalent geometry : bond 0.00301 (15522) covalent geometry : angle 0.49671 (21341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13528.48 seconds wall clock time: 233 minutes 40.02 seconds (14020.02 seconds total)