Starting phenix.real_space_refine on Fri Jul 3 16:15:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gc3_51228/07_2026/9gc3_51228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gc3_51228/07_2026/9gc3_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gc3_51228/07_2026/9gc3_51228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gc3_51228/07_2026/9gc3_51228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gc3_51228/07_2026/9gc3_51228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gc3_51228/07_2026/9gc3_51228.map" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.17, per 1000 atoms: 0.21 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: 1.17 Conformation dependent library (CDL) restraints added in 597.9 milliseconds 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: 1.88 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: 2.80 Time building geometry restraints manager: 1.58 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=" P DT D 67 " pdb=" O5' DT D 67 " ideal model delta sigma weight residual 1.593 1.661 -0.068 1.00e-02 1.00e+04 4.56e+01 bond pdb=" P DA E 24 " pdb=" O5' DA E 24 " ideal model delta sigma weight residual 1.593 1.645 -0.052 1.00e-02 1.00e+04 2.66e+01 bond pdb=" P DT E 20 " pdb=" O5' DT E 20 " ideal model delta sigma weight residual 1.593 1.644 -0.051 1.00e-02 1.00e+04 2.64e+01 bond pdb=" P DC D 69 " pdb=" O5' DC D 69 " ideal model delta sigma weight residual 1.593 1.640 -0.047 1.00e-02 1.00e+04 2.16e+01 ... (remaining 15517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 19404 2.57 - 5.13: 1828 5.13 - 7.70: 94 7.70 - 10.27: 13 10.27 - 12.84: 2 Bond angle restraints: 21341 Sorted by residual: angle pdb=" O4' DT D 67 " pdb=" C1' DT D 67 " pdb=" C2' DT D 67 " ideal model delta sigma weight residual 105.90 100.50 5.40 8.00e-01 1.56e+00 4.56e+01 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=" 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 - 0.130: 2096 0.130 - 0.261: 244 0.261 - 0.391: 39 0.391 - 0.522: 36 0.522 - 0.652: 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 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+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 2.34 2.94 -0.60 2.00e-01 2.50e+01 9.00e+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 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.57e+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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.340 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9343 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= 0.976 Angle : 1.536 12.836 21341 Z= 1.066 Chirality : 0.107 0.652 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.039 0.003 ARG A 405 TYR 0.082 0.009 TYR B 526 PHE 0.043 0.009 PHE A 404 TRP 0.063 0.012 TRP B 297 HIS 0.012 0.003 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.01345 / 0.98 (15522) covalent geometry : angle 1.53632 / 1.07 (21341) hydrogen bonds : bond 0.17778 / 11.42 ( 623) hydrogen bonds : angle 7.30813 / 5.05 ( 1659) *********************** 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 : 0.525 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 115 ASN cc_start: 0.9127 (m110) cc_final: 0.8925 (p0) 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: 0.6582 time to fit residues: 89.6620 Evaluate side-chains 71 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 204 GLN B 311 GLN C 41 GLN C 76 GLN C 106 ASN C 364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.088784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.058497 restraints weight = 30184.707| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.56 r_work: 0.2817 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15522 Z= 0.148 Angle : 0.678 7.917 21341 Z= 0.374 Chirality : 0.049 0.288 2418 Planarity : 0.004 0.051 2417 Dihedral : 21.737 172.626 2680 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.79 % Allowed : 4.17 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1663 helix: 0.46 (0.26), residues: 405 sheet: 0.26 (0.24), residues: 422 loop : -0.00 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 596 TYR 0.016 0.001 TYR B 235 PHE 0.016 0.002 PHE C 441 TRP 0.015 0.002 TRP B 647 HIS 0.004 0.001 HIS B 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (15522) covalent geometry : angle 0.67832 / 0.37 (21341) hydrogen bonds : bond 0.05040 / 3.22 ( 623) hydrogen bonds : angle 5.21853 / 3.68 ( 1659) *********************** 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: 12 poor density : 74 time to evaluate : 0.563 Fit side-chains REVERT: A 132 GLN cc_start: 0.8853 (tt0) cc_final: 0.8554 (tm-30) REVERT: B 152 GLN cc_start: 0.8256 (mt0) cc_final: 0.7919 (mm110) REVERT: C 116 LYS cc_start: 0.8580 (tppp) cc_final: 0.8329 (ttpt) REVERT: C 126 ASN cc_start: 0.7798 (p0) cc_final: 0.7441 (p0) REVERT: C 432 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8656 (mmtp) outliers start: 12 outliers final: 4 residues processed: 82 average time/residue: 0.6094 time to fit residues: 55.1014 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 : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.088301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057913 restraints weight = 30459.729| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.58 r_work: 0.2803 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1935 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= 0.153 Angle : 0.593 6.849 21341 Z= 0.331 Chirality : 0.046 0.294 2418 Planarity : 0.003 0.051 2417 Dihedral : 21.219 173.191 2680 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.86 % Allowed : 5.75 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1663 helix: 0.85 (0.26), residues: 405 sheet: 0.07 (0.23), residues: 448 loop : 0.06 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.014 0.001 TYR B 235 PHE 0.017 0.002 PHE C 441 TRP 0.018 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (15522) covalent geometry : angle 0.59289 / 0.33 (21341) hydrogen bonds : bond 0.04282 / 2.72 ( 623) hydrogen bonds : angle 4.88443 / 3.45 ( 1659) *********************** 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 78 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.566 Fit side-chains REVERT: A 132 GLN cc_start: 0.8862 (tt0) cc_final: 0.8587 (tm-30) REVERT: A 209 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7917 (tm) REVERT: B 152 GLN cc_start: 0.8279 (mt0) cc_final: 0.7947 (mm110) REVERT: C 116 LYS cc_start: 0.8609 (tppp) cc_final: 0.8391 (ttpt) REVERT: C 432 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8540 (mmtp) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 0.5995 time to fit residues: 50.8203 Evaluate side-chains 64 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 226 ILE 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 348 VAL 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 139 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.057269 restraints weight = 30303.923| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.56 r_work: 0.2791 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15522 Z= 0.171 Angle : 0.573 6.469 21341 Z= 0.318 Chirality : 0.045 0.288 2418 Planarity : 0.003 0.053 2417 Dihedral : 21.087 174.284 2680 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.26 % Allowed : 6.22 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1663 helix: 0.98 (0.26), residues: 406 sheet: 0.11 (0.24), residues: 448 loop : 0.06 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 633 TYR 0.014 0.001 TYR A 237 PHE 0.017 0.001 PHE C 441 TRP 0.024 0.002 TRP A 231 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (15522) covalent geometry : angle 0.57252 / 0.32 (21341) hydrogen bonds : bond 0.04041 / 2.57 ( 623) hydrogen bonds : angle 4.75191 / 3.35 ( 1659) *********************** 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 79 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8871 (tt0) cc_final: 0.8606 (tm-30) REVERT: A 188 HIS cc_start: 0.8131 (m-70) cc_final: 0.7875 (m-70) REVERT: B 141 MET cc_start: 0.4488 (ptm) cc_final: 0.4088 (mtp) REVERT: B 152 GLN cc_start: 0.8285 (mt0) cc_final: 0.7974 (mm110) REVERT: B 232 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8464 (mmm-85) REVERT: B 253 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8354 (mtm180) REVERT: C 116 LYS cc_start: 0.8661 (tppp) cc_final: 0.8454 (ttpt) REVERT: C 432 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8529 (mmtm) REVERT: C 502 PHE cc_start: 0.8033 (m-80) cc_final: 0.7686 (m-80) outliers start: 19 outliers final: 8 residues processed: 75 average time/residue: 0.5966 time to fit residues: 49.8752 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 : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS 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 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 117 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 139 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.087991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057493 restraints weight = 30271.642| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.57 r_work: 0.2795 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15522 Z= 0.150 Angle : 0.550 9.422 21341 Z= 0.304 Chirality : 0.044 0.288 2418 Planarity : 0.003 0.046 2417 Dihedral : 20.873 174.054 2680 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.12 % Allowed : 6.55 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1663 helix: 1.12 (0.26), residues: 412 sheet: 0.06 (0.23), residues: 456 loop : 0.14 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.013 0.001 TYR B 235 PHE 0.017 0.001 PHE C 441 TRP 0.024 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15522) covalent geometry : angle 0.54999 / 0.30 (21341) hydrogen bonds : bond 0.03748 / 2.38 ( 623) hydrogen bonds : angle 4.64403 / 3.28 ( 1659) *********************** 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 78 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8845 (tt0) cc_final: 0.8582 (tm-30) REVERT: A 188 HIS cc_start: 0.8152 (m-70) cc_final: 0.7886 (m-70) REVERT: B 141 MET cc_start: 0.4457 (ptm) cc_final: 0.4069 (mtp) REVERT: B 152 GLN cc_start: 0.8277 (mt0) cc_final: 0.7972 (mm110) REVERT: B 232 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8504 (mmm-85) REVERT: B 253 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8392 (mtm180) REVERT: C 432 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8479 (mmtm) REVERT: C 502 PHE cc_start: 0.7980 (m-80) cc_final: 0.7616 (m-80) outliers start: 17 outliers final: 6 residues processed: 73 average time/residue: 0.6237 time to fit residues: 50.7119 Evaluate side-chains 63 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 348 VAL 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 160 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057265 restraints weight = 30148.831| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.57 r_work: 0.2788 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15522 Z= 0.158 Angle : 0.543 8.437 21341 Z= 0.300 Chirality : 0.043 0.288 2418 Planarity : 0.003 0.047 2417 Dihedral : 20.734 174.351 2680 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.86 % Allowed : 7.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1663 helix: 1.23 (0.26), residues: 412 sheet: 0.07 (0.24), residues: 447 loop : 0.16 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 633 TYR 0.012 0.001 TYR B 466 PHE 0.016 0.001 PHE C 441 TRP 0.026 0.001 TRP A 231 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (15522) covalent geometry : angle 0.54283 / 0.30 (21341) hydrogen bonds : bond 0.03771 / 2.41 ( 623) hydrogen bonds : angle 4.59176 / 3.24 ( 1659) *********************** 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 71 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8863 (tt0) cc_final: 0.8611 (tm-30) REVERT: A 188 HIS cc_start: 0.8174 (m-70) cc_final: 0.7923 (m-70) REVERT: A 633 ARG cc_start: 0.8893 (ttp-110) cc_final: 0.8406 (ptp-110) REVERT: B 141 MET cc_start: 0.4407 (ptm) cc_final: 0.4039 (mtp) REVERT: B 152 GLN cc_start: 0.8268 (mt0) cc_final: 0.7975 (mm110) REVERT: B 232 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8538 (mmm-85) REVERT: B 253 ARG cc_start: 0.8747 (mtp85) cc_final: 0.8456 (mtm180) REVERT: C 432 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8601 (mmtm) REVERT: C 502 PHE cc_start: 0.7952 (m-80) cc_final: 0.7570 (m-80) outliers start: 13 outliers final: 8 residues processed: 68 average time/residue: 0.6393 time to fit residues: 48.2224 Evaluate side-chains 67 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 348 VAL 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 169 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 82 optimal weight: 0.0050 chunk 48 optimal weight: 0.2980 overall best weight: 2.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.086921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056403 restraints weight = 30125.830| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.56 r_work: 0.2765 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.2596 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= 0.205 Angle : 0.580 12.496 21341 Z= 0.315 Chirality : 0.044 0.288 2418 Planarity : 0.003 0.055 2417 Dihedral : 20.745 175.358 2680 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.99 % Allowed : 7.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1663 helix: 1.31 (0.26), residues: 409 sheet: 0.06 (0.23), residues: 452 loop : 0.14 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.014 0.001 TYR B 235 PHE 0.015 0.001 PHE C 441 TRP 0.026 0.002 TRP A 231 HIS 0.005 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (15522) covalent geometry : angle 0.58042 / 0.31 (21341) hydrogen bonds : bond 0.04011 / 2.56 ( 623) hydrogen bonds : angle 4.63220 / 3.27 ( 1659) *********************** 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 77 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8853 (tt0) cc_final: 0.8609 (tm-30) REVERT: A 188 HIS cc_start: 0.8263 (m-70) cc_final: 0.8001 (m-70) REVERT: B 141 MET cc_start: 0.4360 (ptm) cc_final: 0.4005 (mtp) REVERT: B 152 GLN cc_start: 0.8305 (mt0) cc_final: 0.8023 (mm110) REVERT: B 232 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8546 (mmm-85) REVERT: B 253 ARG cc_start: 0.8752 (mtp85) cc_final: 0.8471 (mtm180) REVERT: C 126 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7941 (p0) REVERT: C 174 ILE cc_start: 0.9037 (mt) cc_final: 0.8758 (tt) REVERT: C 432 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8611 (mmtm) REVERT: C 502 PHE cc_start: 0.7986 (m-80) cc_final: 0.7550 (m-80) outliers start: 15 outliers final: 7 residues processed: 75 average time/residue: 0.6323 time to fit residues: 52.8077 Evaluate side-chains 70 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 348 VAL 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 139 optimal weight: 0.3980 chunk 170 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 21 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.088219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.057852 restraints weight = 30296.773| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.57 r_work: 0.2804 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2752 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= 0.121 Angle : 0.539 10.507 21341 Z= 0.294 Chirality : 0.042 0.290 2418 Planarity : 0.003 0.035 2417 Dihedral : 20.573 174.737 2680 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1663 helix: 1.38 (0.26), residues: 409 sheet: 0.12 (0.24), residues: 440 loop : 0.18 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 633 TYR 0.013 0.001 TYR B 466 PHE 0.016 0.001 PHE C 441 TRP 0.029 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (15522) covalent geometry : angle 0.53944 / 0.29 (21341) hydrogen bonds : bond 0.03456 / 2.19 ( 623) hydrogen bonds : angle 4.51333 / 3.20 ( 1659) *********************** 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 69 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5513 (tmt) cc_final: 0.5261 (tmt) REVERT: A 132 GLN cc_start: 0.8847 (tt0) cc_final: 0.8602 (tm-30) REVERT: A 188 HIS cc_start: 0.8324 (m-70) cc_final: 0.8080 (m-70) REVERT: A 633 ARG cc_start: 0.8933 (ttp-110) cc_final: 0.8434 (ptp-110) REVERT: B 141 MET cc_start: 0.4200 (ptm) cc_final: 0.3836 (mtp) REVERT: B 152 GLN cc_start: 0.8291 (mt0) cc_final: 0.7994 (mm110) REVERT: B 232 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8533 (mmm-85) REVERT: B 253 ARG cc_start: 0.8784 (mtp85) cc_final: 0.8489 (mtm180) REVERT: C 126 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7786 (p0) REVERT: C 432 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8600 (mmtm) REVERT: C 502 PHE cc_start: 0.7843 (m-80) cc_final: 0.7463 (m-80) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.6361 time to fit residues: 47.3654 Evaluate side-chains 66 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 432 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 75 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.057362 restraints weight = 30082.519| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.56 r_work: 0.2792 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15522 Z= 0.148 Angle : 0.543 11.685 21341 Z= 0.297 Chirality : 0.042 0.289 2418 Planarity : 0.003 0.044 2417 Dihedral : 20.510 175.344 2680 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.60 % Allowed : 8.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.21), residues: 1663 helix: 1.44 (0.26), residues: 408 sheet: 0.16 (0.24), residues: 440 loop : 0.17 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 633 TYR 0.012 0.001 TYR B 466 PHE 0.016 0.001 PHE C 441 TRP 0.030 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (15522) covalent geometry : angle 0.54281 / 0.30 (21341) hydrogen bonds : bond 0.03618 / 2.31 ( 623) hydrogen bonds : angle 4.50376 / 3.19 ( 1659) *********************** 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 69 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5604 (tmt) cc_final: 0.5320 (tmt) REVERT: A 132 GLN cc_start: 0.8849 (tt0) cc_final: 0.8635 (tm-30) REVERT: A 188 HIS cc_start: 0.8335 (m-70) cc_final: 0.8090 (m-70) REVERT: A 596 ARG cc_start: 0.8594 (tpt-90) cc_final: 0.8150 (mmm160) REVERT: A 633 ARG cc_start: 0.8937 (ttp-110) cc_final: 0.8561 (ptp-110) REVERT: B 141 MET cc_start: 0.4137 (ptm) cc_final: 0.3794 (mtp) REVERT: B 152 GLN cc_start: 0.8303 (mt0) cc_final: 0.8008 (mm110) REVERT: B 232 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8542 (mmm-85) REVERT: B 253 ARG cc_start: 0.8790 (mtp85) cc_final: 0.8496 (mtm180) REVERT: C 126 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7862 (p0) REVERT: C 432 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8585 (mmtm) REVERT: C 502 PHE cc_start: 0.7890 (m-80) cc_final: 0.7475 (m-80) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.6400 time to fit residues: 48.3062 Evaluate side-chains 68 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 432 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.087326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056712 restraints weight = 30313.876| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.57 r_work: 0.2772 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15522 Z= 0.188 Angle : 0.565 10.123 21341 Z= 0.307 Chirality : 0.043 0.290 2418 Planarity : 0.003 0.050 2417 Dihedral : 20.563 176.425 2680 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.53 % Allowed : 8.93 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1663 helix: 1.41 (0.26), residues: 409 sheet: 0.14 (0.24), residues: 440 loop : 0.15 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 633 TYR 0.013 0.001 TYR B 466 PHE 0.017 0.001 PHE C 441 TRP 0.031 0.002 TRP A 231 HIS 0.005 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (15522) covalent geometry : angle 0.56535 / 0.31 (21341) hydrogen bonds : bond 0.03829 / 2.45 ( 623) hydrogen bonds : angle 4.54960 / 3.22 ( 1659) ********************** 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 68 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5564 (tmt) cc_final: 0.5247 (tmt) REVERT: A 132 GLN cc_start: 0.8856 (tt0) cc_final: 0.8612 (tm-30) REVERT: A 188 HIS cc_start: 0.8403 (m-70) cc_final: 0.8163 (m-70) REVERT: A 633 ARG cc_start: 0.8934 (ttp-110) cc_final: 0.8553 (ptp-110) REVERT: B 141 MET cc_start: 0.4199 (ptm) cc_final: 0.3853 (mtp) REVERT: B 152 GLN cc_start: 0.8299 (mt0) cc_final: 0.8019 (mm110) REVERT: B 232 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8527 (mmm-85) REVERT: B 253 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8494 (mtm180) REVERT: C 126 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7921 (p0) REVERT: C 174 ILE cc_start: 0.9035 (mt) cc_final: 0.8763 (tt) REVERT: C 432 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8511 (mmtm) REVERT: C 502 PHE cc_start: 0.7915 (m-80) cc_final: 0.7475 (m-80) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.6408 time to fit residues: 48.5685 Evaluate side-chains 67 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 432 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 123 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.088454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.058064 restraints weight = 30066.803| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.57 r_work: 0.2808 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15522 Z= 0.118 Angle : 0.526 9.044 21341 Z= 0.288 Chirality : 0.042 0.288 2418 Planarity : 0.003 0.034 2417 Dihedral : 20.418 175.869 2680 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.46 % Allowed : 9.13 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.21), residues: 1663 helix: 1.50 (0.26), residues: 408 sheet: 0.17 (0.24), residues: 440 loop : 0.17 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 633 TYR 0.012 0.001 TYR B 466 PHE 0.016 0.001 PHE C 441 TRP 0.031 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15522) covalent geometry : angle 0.52618 / 0.29 (21341) hydrogen bonds : bond 0.03387 / 2.17 ( 623) hydrogen bonds : angle 4.45867 / 3.17 ( 1659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5822.38 seconds wall clock time: 99 minutes 53.26 seconds (5993.26 seconds total)