Starting phenix.real_space_refine on Thu Sep 18 07:26:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gc3_51228/09_2025/9gc3_51228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gc3_51228/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gc3_51228/09_2025/9gc3_51228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gc3_51228/09_2025/9gc3_51228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gc3_51228/09_2025/9gc3_51228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gc3_51228/09_2025/9gc3_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-2.0-5805/lib/python3.9/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: 3.89, per 1000 atoms: 0.26 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: 1.29 Conformation dependent library (CDL) restraints added in 644.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.29 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: 3.72 Time building geometry restraints manager: 1.71 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: 2.630 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.100 Find NCS groups from input model: 0.110 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:9.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.01332 (15522) covalent geometry : angle 1.53866 (21341) hydrogen bonds : bond 0.17778 ( 623) hydrogen bonds : angle 7.30813 ( 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 : 0.605 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: 0.8044 time to fit residues: 109.2077 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 : 0.603 ------------------------------------------------------------------------------- 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... 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 = 0.3639 r_free = 0.3639 target = 0.089558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.059250 restraints weight = 30105.416| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.64 r_work: 0.2849 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15522 Z= 0.138 Angle : 0.563 7.998 21341 Z= 0.321 Chirality : 0.041 0.171 2418 Planarity : 0.003 0.042 2417 Dihedral : 20.578 178.889 2680 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.66 % Allowed : 4.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.20), residues: 1663 helix: 0.80 (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 ARG 0.004 0.000 ARG A 596 TYR 0.016 0.001 TYR B 235 PHE 0.015 0.001 PHE C 441 TRP 0.015 0.002 TRP B 647 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00307 (15522) covalent geometry : angle 0.56326 (21341) hydrogen bonds : bond 0.03992 ( 623) hydrogen bonds : angle 4.88389 ( 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 89 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8874 (tt0) cc_final: 0.8575 (tm-30) REVERT: B 152 GLN cc_start: 0.8273 (mt0) cc_final: 0.7959 (mm110) REVERT: B 253 ARG cc_start: 0.8737 (mtp85) cc_final: 0.8482 (mtp85) REVERT: C 116 LYS cc_start: 0.8695 (tppp) cc_final: 0.8478 (ttpt) REVERT: C 126 ASN cc_start: 0.7707 (p0) cc_final: 0.7321 (p0) REVERT: C 432 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8532 (mmtp) REVERT: C 502 PHE cc_start: 0.8046 (m-80) cc_final: 0.7844 (m-80) outliers start: 10 outliers final: 3 residues processed: 87 average time/residue: 0.7180 time to fit residues: 68.7090 Evaluate side-chains 61 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 6 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN B 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.087501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.057065 restraints weight = 30349.369| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.57 r_work: 0.2782 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15522 Z= 0.181 Angle : 0.555 6.931 21341 Z= 0.313 Chirality : 0.043 0.194 2418 Planarity : 0.003 0.061 2417 Dihedral : 20.516 179.580 2680 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.93 % Allowed : 6.28 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.20), residues: 1663 helix: 1.12 (0.26), residues: 406 sheet: 0.23 (0.23), residues: 448 loop : 0.23 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.015 0.001 TYR B 235 PHE 0.014 0.002 PHE B 200 TRP 0.020 0.002 TRP A 231 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00417 (15522) covalent geometry : angle 0.55480 (21341) hydrogen bonds : bond 0.04029 ( 623) hydrogen bonds : angle 4.72536 ( 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 82 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.660 Fit side-chains REVERT: A 132 GLN cc_start: 0.8850 (tt0) cc_final: 0.8578 (tm-30) REVERT: A 612 THR cc_start: 0.9292 (m) cc_final: 0.8979 (t) REVERT: A 633 ARG cc_start: 0.8867 (ptp90) cc_final: 0.8465 (ptp-170) REVERT: B 141 MET cc_start: 0.4489 (ptm) cc_final: 0.4056 (mtp) REVERT: B 152 GLN cc_start: 0.8284 (mt0) cc_final: 0.8001 (mm110) REVERT: C 432 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8579 (mmtm) outliers start: 14 outliers final: 7 residues processed: 77 average time/residue: 0.7341 time to fit residues: 62.2590 Evaluate side-chains 67 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 369 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 139 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 74 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 overall best weight: 0.8098 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.089491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.059271 restraints weight = 30375.031| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.62 r_work: 0.2851 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15522 Z= 0.117 Angle : 0.496 7.487 21341 Z= 0.280 Chirality : 0.040 0.150 2418 Planarity : 0.003 0.035 2417 Dihedral : 19.951 179.056 2680 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.86 % Allowed : 7.01 % Favored : 92.13 % 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 aren not related in a simple way. whole: 0.70 (0.20), residues: 1663 helix: 1.46 (0.26), residues: 401 sheet: 0.22 (0.23), residues: 461 loop : 0.25 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 232 TYR 0.013 0.001 TYR B 235 PHE 0.014 0.001 PHE C 441 TRP 0.023 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00258 (15522) covalent geometry : angle 0.49607 (21341) hydrogen bonds : bond 0.03234 ( 623) hydrogen bonds : angle 4.44061 ( 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 78 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8799 (tt0) cc_final: 0.8518 (tm-30) REVERT: A 612 THR cc_start: 0.9264 (m) cc_final: 0.8956 (t) REVERT: B 141 MET cc_start: 0.4227 (ptm) cc_final: 0.3863 (mtp) REVERT: B 152 GLN cc_start: 0.8371 (mt0) cc_final: 0.8136 (mm110) REVERT: B 253 ARG cc_start: 0.8754 (mtp85) cc_final: 0.8329 (mtm180) REVERT: C 351 MET cc_start: 0.8936 (mtm) cc_final: 0.8670 (mtm) REVERT: C 432 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8586 (mmtm) REVERT: C 502 PHE cc_start: 0.7802 (m-80) cc_final: 0.7464 (m-80) outliers start: 13 outliers final: 8 residues processed: 74 average time/residue: 0.6876 time to fit residues: 56.5786 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 : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 365 SER Chi-restraints excluded: chain C residue 369 MET 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: 9.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.087193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.056755 restraints weight = 30310.382| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.57 r_work: 0.2773 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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 0.038 15522 Z= 0.191 Angle : 0.534 9.641 21341 Z= 0.299 Chirality : 0.042 0.187 2418 Planarity : 0.003 0.056 2417 Dihedral : 20.187 178.061 2680 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.93 % Allowed : 7.34 % Favored : 91.73 % 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 aren not related in a simple way. whole: 0.67 (0.20), residues: 1663 helix: 1.45 (0.26), residues: 402 sheet: 0.24 (0.24), residues: 447 loop : 0.18 (0.22), residues: 814 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 0.014 0.001 PHE C 441 TRP 0.023 0.001 TRP A 231 HIS 0.005 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00441 (15522) covalent geometry : angle 0.53427 (21341) hydrogen bonds : bond 0.03746 ( 623) hydrogen bonds : angle 4.56319 ( 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 75 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.618 Fit side-chains REVERT: A 132 GLN cc_start: 0.8895 (tt0) cc_final: 0.8656 (tm-30) REVERT: A 612 THR cc_start: 0.9276 (m) cc_final: 0.8997 (t) REVERT: A 633 ARG cc_start: 0.8880 (ptp90) cc_final: 0.8657 (ptp-110) REVERT: B 141 MET cc_start: 0.4230 (ptm) cc_final: 0.3859 (mtp) REVERT: B 152 GLN cc_start: 0.8315 (mt0) cc_final: 0.8076 (mm110) REVERT: B 253 ARG cc_start: 0.8751 (mtp85) cc_final: 0.8460 (mtm180) REVERT: C 432 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8632 (mmtm) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.6591 time to fit residues: 51.4410 Evaluate side-chains 70 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 365 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 160 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.086837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.056378 restraints weight = 30159.022| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.56 r_work: 0.2764 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2890 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= 0.203 Angle : 0.548 10.114 21341 Z= 0.303 Chirality : 0.042 0.190 2418 Planarity : 0.003 0.056 2417 Dihedral : 20.151 177.228 2680 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.06 % Allowed : 7.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.20), residues: 1663 helix: 1.37 (0.26), residues: 409 sheet: 0.23 (0.24), residues: 443 loop : 0.21 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.013 0.001 TYR B 235 PHE 0.014 0.001 PHE C 441 TRP 0.025 0.002 TRP A 231 HIS 0.005 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00471 (15522) covalent geometry : angle 0.54793 (21341) hydrogen bonds : bond 0.03824 ( 623) hydrogen bonds : angle 4.58731 ( 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 83 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.632 Fit side-chains REVERT: A 132 GLN cc_start: 0.8888 (tt0) cc_final: 0.8620 (tm-30) REVERT: A 612 THR cc_start: 0.9301 (m) cc_final: 0.9035 (t) REVERT: A 633 ARG cc_start: 0.8884 (ptp90) cc_final: 0.8649 (ptp-110) REVERT: B 141 MET cc_start: 0.4240 (ptm) cc_final: 0.3868 (mtp) REVERT: B 152 GLN cc_start: 0.8278 (mt0) cc_final: 0.8012 (mm110) REVERT: B 253 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8457 (mtm180) REVERT: C 126 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7908 (p0) REVERT: C 174 ILE cc_start: 0.9010 (mt) cc_final: 0.8731 (tt) REVERT: C 351 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8794 (mtm) REVERT: C 432 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8564 (mmtp) REVERT: C 497 LEU cc_start: 0.9141 (tp) cc_final: 0.8892 (tm) REVERT: C 502 PHE cc_start: 0.7897 (m-80) cc_final: 0.7481 (m-80) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.6940 time to fit residues: 59.2950 Evaluate side-chains 77 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 6.9990 chunk 41 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.087660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057259 restraints weight = 30227.666| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.57 r_work: 0.2788 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15522 Z= 0.166 Angle : 0.529 11.100 21341 Z= 0.292 Chirality : 0.041 0.159 2418 Planarity : 0.003 0.048 2417 Dihedral : 19.988 177.511 2680 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.19 % Allowed : 7.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1663 helix: 1.44 (0.26), residues: 409 sheet: 0.19 (0.24), residues: 434 loop : 0.25 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.012 0.001 TYR B 235 PHE 0.014 0.001 PHE C 441 TRP 0.027 0.001 TRP A 231 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00383 (15522) covalent geometry : angle 0.52905 (21341) hydrogen bonds : bond 0.03544 ( 623) hydrogen bonds : angle 4.49722 ( 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 83 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.617 Fit side-chains REVERT: A 132 GLN cc_start: 0.8851 (tt0) cc_final: 0.8596 (tm-30) REVERT: A 596 ARG cc_start: 0.8567 (tpt-90) cc_final: 0.8145 (mmm160) REVERT: A 612 THR cc_start: 0.9271 (m) cc_final: 0.9027 (t) REVERT: A 633 ARG cc_start: 0.8901 (ptp90) cc_final: 0.8662 (ptp-110) REVERT: B 141 MET cc_start: 0.4290 (ptm) cc_final: 0.3902 (mtp) REVERT: B 152 GLN cc_start: 0.8293 (mt0) cc_final: 0.8005 (mm110) REVERT: B 253 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8502 (mtm180) REVERT: C 1 MET cc_start: 0.7041 (mtm) cc_final: 0.6831 (mtt) REVERT: C 126 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7893 (p0) REVERT: C 174 ILE cc_start: 0.9003 (mt) cc_final: 0.8744 (tt) REVERT: C 351 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8744 (mtm) REVERT: C 432 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8584 (mmtp) REVERT: C 497 LEU cc_start: 0.9176 (tp) cc_final: 0.8941 (tm) REVERT: C 502 PHE cc_start: 0.7798 (m-80) cc_final: 0.7399 (m-80) outliers start: 18 outliers final: 11 residues processed: 76 average time/residue: 0.6822 time to fit residues: 57.4216 Evaluate side-chains 78 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 365 SER Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 463 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.0570 chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.089787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059654 restraints weight = 30495.857| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.62 r_work: 0.2850 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15522 Z= 0.106 Angle : 0.490 12.002 21341 Z= 0.271 Chirality : 0.040 0.136 2418 Planarity : 0.003 0.034 2417 Dihedral : 19.678 178.146 2680 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.79 % Allowed : 8.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1663 helix: 1.62 (0.26), residues: 408 sheet: 0.17 (0.24), residues: 444 loop : 0.29 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 232 TYR 0.012 0.001 TYR B 235 PHE 0.014 0.001 PHE C 441 TRP 0.030 0.001 TRP A 231 HIS 0.003 0.000 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00235 (15522) covalent geometry : angle 0.48955 (21341) hydrogen bonds : bond 0.03015 ( 623) hydrogen bonds : angle 4.29564 ( 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 82 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.619 Fit side-chains REVERT: A 1 MET cc_start: 0.5380 (tmt) cc_final: 0.5102 (tmt) REVERT: A 132 GLN cc_start: 0.8816 (tt0) cc_final: 0.8575 (tm-30) REVERT: A 198 ARG cc_start: 0.9236 (tpp-160) cc_final: 0.8166 (tmm160) REVERT: A 596 ARG cc_start: 0.8534 (tpt-90) cc_final: 0.8157 (mmm160) REVERT: A 612 THR cc_start: 0.9217 (m) cc_final: 0.8949 (t) REVERT: A 633 ARG cc_start: 0.8962 (ptp90) cc_final: 0.8491 (ptp-170) REVERT: B 141 MET cc_start: 0.4062 (ptm) cc_final: 0.3695 (mtp) REVERT: B 152 GLN cc_start: 0.8393 (mt0) cc_final: 0.8170 (mm110) REVERT: B 253 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8409 (mtm180) REVERT: C 1 MET cc_start: 0.7004 (mtm) cc_final: 0.6776 (mtt) REVERT: C 126 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7660 (p0) REVERT: C 174 ILE cc_start: 0.8927 (mt) cc_final: 0.8724 (tt) REVERT: C 351 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8617 (mtm) REVERT: C 432 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8608 (mmtm) REVERT: C 497 LEU cc_start: 0.9158 (tp) cc_final: 0.8931 (tm) REVERT: C 502 PHE cc_start: 0.7581 (m-80) cc_final: 0.7239 (m-80) outliers start: 12 outliers final: 6 residues processed: 76 average time/residue: 0.6710 time to fit residues: 56.4793 Evaluate side-chains 74 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 75 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 170 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.089653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059830 restraints weight = 30575.757| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.59 r_work: 0.2857 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15522 Z= 0.107 Angle : 0.494 11.941 21341 Z= 0.269 Chirality : 0.040 0.138 2418 Planarity : 0.003 0.034 2417 Dihedral : 19.620 176.934 2680 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.21), residues: 1663 helix: 1.72 (0.26), residues: 407 sheet: 0.27 (0.24), residues: 449 loop : 0.23 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 232 TYR 0.012 0.001 TYR B 235 PHE 0.013 0.001 PHE C 441 TRP 0.032 0.001 TRP A 231 HIS 0.005 0.000 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00237 (15522) covalent geometry : angle 0.49384 (21341) hydrogen bonds : bond 0.02946 ( 623) hydrogen bonds : angle 4.23252 ( 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 80 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8809 (tt0) cc_final: 0.8541 (tm-30) REVERT: A 198 ARG cc_start: 0.9230 (tpp-160) cc_final: 0.8174 (tmm160) REVERT: A 596 ARG cc_start: 0.8545 (tpt-90) cc_final: 0.8192 (mmm160) REVERT: A 612 THR cc_start: 0.9178 (m) cc_final: 0.8915 (t) REVERT: B 141 MET cc_start: 0.4016 (ptm) cc_final: 0.3633 (mtp) REVERT: B 152 GLN cc_start: 0.8428 (mt0) cc_final: 0.8207 (mm110) REVERT: B 253 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8426 (mtm180) REVERT: C 126 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7696 (p0) REVERT: C 207 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8721 (mpp) REVERT: C 351 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8620 (mtm) REVERT: C 432 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8640 (mmtm) REVERT: C 497 LEU cc_start: 0.9163 (tp) cc_final: 0.8908 (tm) REVERT: C 502 PHE cc_start: 0.7589 (m-80) cc_final: 0.7278 (m-80) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.6858 time to fit residues: 57.1046 Evaluate side-chains 74 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 146 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 156 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.085903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.055461 restraints weight = 30499.775| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.59 r_work: 0.2744 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15522 Z= 0.290 Angle : 0.610 12.295 21341 Z= 0.329 Chirality : 0.045 0.235 2418 Planarity : 0.004 0.064 2417 Dihedral : 20.190 174.612 2680 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.20), residues: 1663 helix: 1.40 (0.26), residues: 408 sheet: 0.25 (0.24), residues: 443 loop : 0.12 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 281 TYR 0.015 0.002 TYR B 235 PHE 0.015 0.002 PHE C 441 TRP 0.031 0.002 TRP A 231 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00677 (15522) covalent geometry : angle 0.61001 (21341) hydrogen bonds : bond 0.04182 ( 623) hydrogen bonds : angle 4.68438 ( 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 75 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.652 Fit side-chains REVERT: A 1 MET cc_start: 0.5442 (tmt) cc_final: 0.5027 (tmt) REVERT: A 132 GLN cc_start: 0.8852 (tt0) cc_final: 0.8556 (tm-30) REVERT: A 541 ASN cc_start: 0.7469 (m-40) cc_final: 0.7240 (t0) REVERT: A 612 THR cc_start: 0.9258 (m) cc_final: 0.9025 (t) REVERT: A 633 ARG cc_start: 0.8901 (ptp90) cc_final: 0.8663 (ptp-110) REVERT: B 141 MET cc_start: 0.4186 (ptm) cc_final: 0.3813 (mtp) REVERT: B 152 GLN cc_start: 0.8309 (mt0) cc_final: 0.7988 (mm110) REVERT: B 253 ARG cc_start: 0.8823 (mtp85) cc_final: 0.8561 (mtp85) REVERT: C 126 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8133 (p0) REVERT: C 351 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8787 (mtm) REVERT: C 432 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8560 (mmtp) outliers start: 12 outliers final: 8 residues processed: 70 average time/residue: 0.6937 time to fit residues: 53.8028 Evaluate side-chains 71 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU 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 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: 3.9990 chunk 112 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 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 = 0.088308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058578 restraints weight = 30098.135| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.55 r_work: 0.2826 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3348 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= 0.123 Angle : 0.512 12.330 21341 Z= 0.280 Chirality : 0.040 0.141 2418 Planarity : 0.003 0.035 2417 Dihedral : 19.746 176.679 2680 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.66 % Allowed : 8.93 % 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 aren not related in a simple way. whole: 0.72 (0.21), residues: 1663 helix: 1.60 (0.27), residues: 408 sheet: 0.19 (0.23), residues: 456 loop : 0.20 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 435 TYR 0.012 0.001 TYR B 235 PHE 0.014 0.001 PHE C 441 TRP 0.032 0.001 TRP A 231 HIS 0.005 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00279 (15522) covalent geometry : angle 0.51221 (21341) hydrogen bonds : bond 0.03176 ( 623) hydrogen bonds : angle 4.40761 ( 1659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6750.73 seconds wall clock time: 115 minutes 43.82 seconds (6943.82 seconds total)