Starting phenix.real_space_refine on Mon Jul 28 18:23:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbg_61313/07_2025/9jbg_61313.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbg_61313/07_2025/9jbg_61313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jbg_61313/07_2025/9jbg_61313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbg_61313/07_2025/9jbg_61313.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbg_61313/07_2025/9jbg_61313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbg_61313/07_2025/9jbg_61313.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.026 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 5 5.49 5 S 65 5.16 5 C 6812 2.51 5 N 1564 2.21 5 O 1741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10187 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5452 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 21, 'TRANS': 669} Chain breaks: 2 Chain: "B" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4454 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 21, 'TRANS': 546} Chain breaks: 2 Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'3PE': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 125 Unusual residues: {'3PE': 1, 'OLA': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.96, per 1000 atoms: 0.78 Number of scatterers: 10187 At special positions: 0 Unit cell: (95.344, 99.384, 130.088, 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 65 16.00 P 5 15.00 O 1741 8.00 N 1564 7.00 C 6812 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 1 sheets defined 79.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.779A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.925A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 124 Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.675A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.586A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.750A pdb=" N ILE A 183 " --> pdb=" O MET A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.886A pdb=" N VAL A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 Processing helix chain 'A' and resid 238 through 250 removed outlier: 3.790A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 320 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.021A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 367 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 371 through 405 Processing helix chain 'A' and resid 411 through 435 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 449 through 473 removed outlier: 3.634A pdb=" N SER A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 518 through 544 Processing helix chain 'A' and resid 639 through 653 removed outlier: 4.289A pdb=" N GLU A 643 " --> pdb=" O ILE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 removed outlier: 3.629A pdb=" N HIS A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 711 removed outlier: 3.592A pdb=" N GLU A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 758 Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.590A pdb=" N VAL A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.718A pdb=" N VAL B 53 " --> pdb=" O CYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.864A pdb=" N LYS B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.588A pdb=" N ASN B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 125 removed outlier: 3.774A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 164 through 196 removed outlier: 3.796A pdb=" N TYR B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 5.088A pdb=" N ASN B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Proline residue: B 182 - end of helix removed outlier: 3.591A pdb=" N GLU B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.516A pdb=" N PHE B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.096A pdb=" N ASN B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.731A pdb=" N GLY B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 removed outlier: 3.609A pdb=" N LEU B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.543A pdb=" N GLU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.909A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 367 removed outlier: 3.745A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix removed outlier: 3.519A pdb=" N TYR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 404 removed outlier: 3.900A pdb=" N ILE B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 435 removed outlier: 3.576A pdb=" N ASN B 417 " --> pdb=" O MET B 413 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N MET B 429 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET B 430 " --> pdb=" O CYS B 426 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN B 433 " --> pdb=" O MET B 429 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 446 Processing helix chain 'B' and resid 446 through 472 removed outlier: 4.337A pdb=" N LEU B 450 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 removed outlier: 3.718A pdb=" N TRP B 489 " --> pdb=" O ILE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.703A pdb=" N VAL B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 544 removed outlier: 3.947A pdb=" N LEU B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE B 529 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET B 540 " --> pdb=" O GLY B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 682 removed outlier: 3.988A pdb=" N VAL B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TRP B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU B 680 " --> pdb=" O CYS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 701 Processing helix chain 'B' and resid 703 through 712 removed outlier: 3.692A pdb=" N SER B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 709 " --> pdb=" O PHE B 705 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 710 " --> pdb=" O ILE B 706 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 780 through 782 649 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1515 1.31 - 1.43: 2783 1.43 - 1.56: 6005 1.56 - 1.69: 11 1.69 - 1.82: 100 Bond restraints: 10414 Sorted by residual: bond pdb=" C10 OLA B 902 " pdb=" C9 OLA B 902 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C MET B 90 " pdb=" O MET B 90 " ideal model delta sigma weight residual 1.236 1.179 0.057 1.15e-02 7.56e+03 2.49e+01 bond pdb=" C ASN B 181 " pdb=" O ASN B 181 " ideal model delta sigma weight residual 1.243 1.213 0.030 9.50e-03 1.11e+04 1.02e+01 bond pdb=" N ILE A 169 " pdb=" CA ILE A 169 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.27e+00 bond pdb=" N ILE A 357 " pdb=" CA ILE A 357 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.00e+00 ... (remaining 10409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 13155 1.89 - 3.79: 727 3.79 - 5.68: 152 5.68 - 7.58: 27 7.58 - 9.47: 7 Bond angle restraints: 14068 Sorted by residual: angle pdb=" N THR A 461 " pdb=" CA THR A 461 " pdb=" C THR A 461 " ideal model delta sigma weight residual 111.36 104.92 6.44 1.09e+00 8.42e-01 3.50e+01 angle pdb=" N ILE B 522 " pdb=" CA ILE B 522 " pdb=" C ILE B 522 " ideal model delta sigma weight residual 110.53 105.42 5.11 9.40e-01 1.13e+00 2.95e+01 angle pdb=" CA PRO A 327 " pdb=" N PRO A 327 " pdb=" CD PRO A 327 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" N VAL A 448 " pdb=" CA VAL A 448 " pdb=" C VAL A 448 " ideal model delta sigma weight residual 113.07 105.95 7.12 1.37e+00 5.33e-01 2.70e+01 angle pdb=" C ASN B 439 " pdb=" CA ASN B 439 " pdb=" CB ASN B 439 " ideal model delta sigma weight residual 117.23 110.21 7.02 1.36e+00 5.41e-01 2.67e+01 ... (remaining 14063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 5841 30.95 - 61.90: 331 61.90 - 92.86: 23 92.86 - 123.81: 8 123.81 - 154.76: 3 Dihedral angle restraints: 6206 sinusoidal: 2553 harmonic: 3653 Sorted by residual: dihedral pdb=" CA THR A 369 " pdb=" C THR A 369 " pdb=" N MET A 370 " pdb=" CA MET A 370 " ideal model delta harmonic sigma weight residual 180.00 152.24 27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" C21 P5S A 903 " pdb=" C22 P5S A 903 " pdb=" C23 P5S A 903 " pdb=" C24 P5S A 903 " ideal model delta sinusoidal sigma weight residual -64.63 90.13 -154.76 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C38 P5S A 903 " pdb=" C39 P5S A 903 " pdb=" C40 P5S A 903 " pdb=" C41 P5S A 903 " ideal model delta sinusoidal sigma weight residual 64.51 -73.40 137.91 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 6203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1143 0.050 - 0.101: 348 0.101 - 0.151: 97 0.151 - 0.202: 45 0.202 - 0.252: 6 Chirality restraints: 1639 Sorted by residual: chirality pdb=" CG LEU A 215 " pdb=" CB LEU A 215 " pdb=" CD1 LEU A 215 " pdb=" CD2 LEU A 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE B 190 " pdb=" N ILE B 190 " pdb=" C ILE B 190 " pdb=" CB ILE B 190 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE B 710 " pdb=" N ILE B 710 " pdb=" C ILE B 710 " pdb=" CB ILE B 710 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1636 not shown) Planarity restraints: 1687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 902 " 0.157 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C11 OLA B 902 " -0.073 2.00e-02 2.50e+03 pdb=" C8 OLA B 902 " 0.072 2.00e-02 2.50e+03 pdb=" C9 OLA B 902 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 326 " -0.082 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO A 327 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 181 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ASN B 181 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN B 181 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO B 182 " -0.020 2.00e-02 2.50e+03 ... (remaining 1684 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1627 2.76 - 3.29: 11431 3.29 - 3.83: 17419 3.83 - 4.36: 21575 4.36 - 4.90: 33400 Nonbonded interactions: 85452 Sorted by model distance: nonbonded pdb=" OD1 ASP A 99 " pdb=" OG SER A 101 " model vdw 2.222 3.040 nonbonded pdb=" O LEU A 454 " pdb=" OG1 THR A 457 " model vdw 2.236 3.040 nonbonded pdb=" OD2 ASP B 146 " pdb=" OH TYR B 320 " model vdw 2.239 3.040 nonbonded pdb=" O HIS B 412 " pdb=" OG1 THR B 415 " model vdw 2.260 3.040 nonbonded pdb=" O SER A 453 " pdb=" OG SER A 456 " model vdw 2.295 3.040 ... (remaining 85447 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 group one per residue 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: 3.810 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.006 0.137 10414 Z= 0.385 Angle : 0.980 9.473 14068 Z= 0.649 Chirality : 0.059 0.252 1639 Planarity : 0.008 0.122 1687 Dihedral : 18.836 154.759 3852 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.73 % Allowed : 26.07 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1247 helix: -0.15 (0.18), residues: 896 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 679 HIS 0.006 0.001 HIS A 716 PHE 0.034 0.002 PHE B 276 TYR 0.020 0.001 TYR A 458 ARG 0.009 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.20402 ( 649) hydrogen bonds : angle 7.91297 ( 1947) covalent geometry : bond 0.00592 (10414) covalent geometry : angle 0.98007 (14068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 245 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8063 (t80) cc_final: 0.7733 (t80) REVERT: A 413 MET cc_start: 0.6894 (mtm) cc_final: 0.6413 (mpp) REVERT: A 816 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: B 165 TYR cc_start: 0.7759 (m-10) cc_final: 0.6548 (m-10) outliers start: 19 outliers final: 7 residues processed: 255 average time/residue: 0.1875 time to fit residues: 70.5897 Evaluate side-chains 226 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 218 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 191 GLN A 198 ASN A 337 ASN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN A 693 GLN ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 417 ASN B 439 ASN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.132608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108038 restraints weight = 30033.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.110715 restraints weight = 16746.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.112445 restraints weight = 11235.800| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10414 Z= 0.160 Angle : 0.699 14.217 14068 Z= 0.351 Chirality : 0.044 0.194 1639 Planarity : 0.005 0.066 1687 Dihedral : 14.843 179.337 1618 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.29 % Allowed : 21.15 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1247 helix: 0.36 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -2.15 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 679 HIS 0.005 0.001 HIS A 716 PHE 0.039 0.002 PHE A 367 TYR 0.044 0.002 TYR A 458 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.05530 ( 649) hydrogen bonds : angle 5.57490 ( 1947) covalent geometry : bond 0.00347 (10414) covalent geometry : angle 0.69917 (14068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.7203 (m-80) cc_final: 0.6959 (m-80) REVERT: A 219 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7093 (mm) REVERT: A 318 PHE cc_start: 0.8074 (t80) cc_final: 0.7703 (t80) REVERT: A 413 MET cc_start: 0.6903 (mtm) cc_final: 0.6469 (mpp) REVERT: A 429 MET cc_start: 0.8978 (tpt) cc_final: 0.8378 (tpt) REVERT: A 447 PHE cc_start: 0.7654 (p90) cc_final: 0.7304 (p90) REVERT: A 797 SER cc_start: 0.4904 (OUTLIER) cc_final: 0.4393 (p) REVERT: B 674 SER cc_start: 0.9179 (t) cc_final: 0.8872 (p) REVERT: B 705 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7596 (m-80) outliers start: 58 outliers final: 30 residues processed: 278 average time/residue: 0.1777 time to fit residues: 73.9348 Evaluate side-chains 245 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 695 PHE Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 216 GLN A 337 ASN A 380 GLN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 816 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN B 700 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.132565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.108207 restraints weight = 30286.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110970 restraints weight = 16666.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.112739 restraints weight = 11069.151| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10414 Z= 0.145 Angle : 0.691 13.206 14068 Z= 0.341 Chirality : 0.043 0.249 1639 Planarity : 0.005 0.056 1687 Dihedral : 13.915 174.605 1604 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.29 % Allowed : 22.15 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1247 helix: 0.52 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -2.15 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 679 HIS 0.004 0.001 HIS A 716 PHE 0.031 0.002 PHE B 529 TYR 0.055 0.001 TYR A 458 ARG 0.004 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 649) hydrogen bonds : angle 5.34523 ( 1947) covalent geometry : bond 0.00315 (10414) covalent geometry : angle 0.69114 (14068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7810 (ttm110) REVERT: A 219 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7173 (mm) REVERT: A 413 MET cc_start: 0.6894 (mtm) cc_final: 0.6486 (mpp) REVERT: A 429 MET cc_start: 0.8906 (tpt) cc_final: 0.8405 (tpt) REVERT: A 430 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8609 (mpp) REVERT: A 440 PHE cc_start: 0.6144 (t80) cc_final: 0.5926 (t80) REVERT: A 447 PHE cc_start: 0.7626 (p90) cc_final: 0.7345 (p90) REVERT: A 797 SER cc_start: 0.4791 (OUTLIER) cc_final: 0.4264 (p) REVERT: B 178 MET cc_start: 0.8262 (mmm) cc_final: 0.7622 (ttt) REVERT: B 521 MET cc_start: 0.8174 (ttt) cc_final: 0.7568 (tpt) REVERT: B 674 SER cc_start: 0.9170 (t) cc_final: 0.8854 (p) REVERT: B 699 PHE cc_start: 0.6999 (t80) cc_final: 0.6163 (t80) REVERT: B 705 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7662 (m-80) outliers start: 58 outliers final: 37 residues processed: 274 average time/residue: 0.1860 time to fit residues: 76.4726 Evaluate side-chains 264 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 695 PHE Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 25 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.132318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.108023 restraints weight = 29841.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110800 restraints weight = 16409.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112557 restraints weight = 10873.686| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10414 Z= 0.146 Angle : 0.691 14.069 14068 Z= 0.341 Chirality : 0.043 0.182 1639 Planarity : 0.005 0.056 1687 Dihedral : 13.722 170.198 1604 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.83 % Allowed : 23.97 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1247 helix: 0.53 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -2.09 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 460 HIS 0.004 0.001 HIS B 412 PHE 0.033 0.002 PHE B 529 TYR 0.050 0.001 TYR A 458 ARG 0.002 0.000 ARG A 832 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 649) hydrogen bonds : angle 5.24601 ( 1947) covalent geometry : bond 0.00322 (10414) covalent geometry : angle 0.69131 (14068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7002 (mm) REVERT: A 413 MET cc_start: 0.6866 (mtm) cc_final: 0.6456 (mpp) REVERT: A 440 PHE cc_start: 0.6124 (t80) cc_final: 0.5905 (t80) REVERT: A 447 PHE cc_start: 0.7603 (p90) cc_final: 0.7312 (p90) REVERT: A 657 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7659 (mtt180) REVERT: A 797 SER cc_start: 0.4770 (OUTLIER) cc_final: 0.4227 (p) REVERT: B 178 MET cc_start: 0.8317 (mmm) cc_final: 0.7577 (ttt) REVERT: B 299 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6412 (tm-30) REVERT: B 364 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8737 (mm) REVERT: B 380 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8352 (pp30) REVERT: B 521 MET cc_start: 0.8326 (ttt) cc_final: 0.7854 (tpt) REVERT: B 674 SER cc_start: 0.9116 (t) cc_final: 0.8809 (p) REVERT: B 705 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7790 (m-80) outliers start: 53 outliers final: 39 residues processed: 264 average time/residue: 0.2296 time to fit residues: 93.0799 Evaluate side-chains 266 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 695 PHE Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 0.1980 chunk 72 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.133533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.109016 restraints weight = 29907.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111826 restraints weight = 16437.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.113585 restraints weight = 10923.517| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10414 Z= 0.132 Angle : 0.693 13.777 14068 Z= 0.336 Chirality : 0.043 0.192 1639 Planarity : 0.005 0.055 1687 Dihedral : 13.359 171.636 1604 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.74 % Allowed : 26.16 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1247 helix: 0.59 (0.17), residues: 946 sheet: None (None), residues: 0 loop : -2.00 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 679 HIS 0.003 0.001 HIS A 658 PHE 0.031 0.002 PHE B 529 TYR 0.046 0.001 TYR A 458 ARG 0.002 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 649) hydrogen bonds : angle 5.11312 ( 1947) covalent geometry : bond 0.00283 (10414) covalent geometry : angle 0.69320 (14068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: A 219 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6932 (mm) REVERT: A 413 MET cc_start: 0.6816 (mtm) cc_final: 0.6439 (mpp) REVERT: A 429 MET cc_start: 0.8770 (tpt) cc_final: 0.8418 (tpt) REVERT: A 430 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8559 (mpp) REVERT: A 440 PHE cc_start: 0.6165 (t80) cc_final: 0.5943 (t80) REVERT: A 447 PHE cc_start: 0.7542 (p90) cc_final: 0.7255 (p90) REVERT: A 471 LEU cc_start: 0.3848 (OUTLIER) cc_final: 0.3452 (mm) REVERT: A 657 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7620 (mtt180) REVERT: A 703 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7904 (mm-40) REVERT: A 797 SER cc_start: 0.4860 (OUTLIER) cc_final: 0.4408 (p) REVERT: B 299 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6300 (tm-30) REVERT: B 364 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8630 (mm) REVERT: B 674 SER cc_start: 0.9147 (t) cc_final: 0.8878 (p) REVERT: B 705 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7953 (m-80) outliers start: 52 outliers final: 32 residues processed: 275 average time/residue: 0.2904 time to fit residues: 120.1949 Evaluate side-chains 263 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 695 PHE Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.130346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105882 restraints weight = 30624.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108568 restraints weight = 16921.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.110267 restraints weight = 11266.102| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10414 Z= 0.183 Angle : 0.740 12.276 14068 Z= 0.363 Chirality : 0.045 0.230 1639 Planarity : 0.005 0.060 1687 Dihedral : 13.571 162.230 1604 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.65 % Allowed : 26.71 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1247 helix: 0.50 (0.17), residues: 952 sheet: None (None), residues: 0 loop : -2.10 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 460 HIS 0.002 0.001 HIS B 658 PHE 0.035 0.002 PHE B 529 TYR 0.045 0.002 TYR A 458 ARG 0.004 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 649) hydrogen bonds : angle 5.31066 ( 1947) covalent geometry : bond 0.00417 (10414) covalent geometry : angle 0.73973 (14068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 236 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 TYR cc_start: 0.8368 (t80) cc_final: 0.8076 (t80) REVERT: A 216 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: A 219 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7101 (mm) REVERT: A 347 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7559 (tpp) REVERT: A 440 PHE cc_start: 0.6160 (t80) cc_final: 0.5945 (t80) REVERT: A 447 PHE cc_start: 0.7567 (p90) cc_final: 0.7210 (p90) REVERT: A 459 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8777 (mm) REVERT: A 471 LEU cc_start: 0.3854 (OUTLIER) cc_final: 0.3498 (mm) REVERT: A 699 PHE cc_start: 0.5873 (t80) cc_final: 0.5425 (t80) REVERT: A 797 SER cc_start: 0.4492 (OUTLIER) cc_final: 0.3929 (p) REVERT: B 178 MET cc_start: 0.8308 (mmm) cc_final: 0.7578 (ttt) REVERT: B 380 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8383 (pp30) REVERT: B 521 MET cc_start: 0.8183 (ttt) cc_final: 0.7696 (tpt) REVERT: B 674 SER cc_start: 0.8981 (t) cc_final: 0.8718 (p) REVERT: B 705 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8024 (m-80) outliers start: 62 outliers final: 42 residues processed: 268 average time/residue: 0.2531 time to fit residues: 102.1612 Evaluate side-chains 267 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 695 PHE Chi-restraints excluded: chain B residue 696 CYS Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.132086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.108018 restraints weight = 30509.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110817 restraints weight = 16607.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112591 restraints weight = 10922.386| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10414 Z= 0.148 Angle : 0.748 11.613 14068 Z= 0.361 Chirality : 0.044 0.204 1639 Planarity : 0.005 0.059 1687 Dihedral : 13.242 162.737 1604 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.56 % Allowed : 28.44 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1247 helix: 0.55 (0.17), residues: 953 sheet: None (None), residues: 0 loop : -2.04 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 679 HIS 0.003 0.001 HIS A 658 PHE 0.028 0.002 PHE B 529 TYR 0.043 0.001 TYR A 458 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 649) hydrogen bonds : angle 5.22681 ( 1947) covalent geometry : bond 0.00334 (10414) covalent geometry : angle 0.74834 (14068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TRP cc_start: 0.5408 (OUTLIER) cc_final: 0.4281 (m-10) REVERT: A 151 TYR cc_start: 0.8449 (t80) cc_final: 0.8124 (t80) REVERT: A 216 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: A 219 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7119 (mm) REVERT: A 413 MET cc_start: 0.6946 (mtt) cc_final: 0.6385 (mpp) REVERT: A 447 PHE cc_start: 0.7532 (p90) cc_final: 0.7228 (p90) REVERT: A 459 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8844 (mm) REVERT: A 471 LEU cc_start: 0.3870 (OUTLIER) cc_final: 0.3506 (mm) REVERT: A 657 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7581 (mtt180) REVERT: A 797 SER cc_start: 0.4353 (OUTLIER) cc_final: 0.3766 (p) REVERT: B 178 MET cc_start: 0.8310 (mmm) cc_final: 0.7561 (ttt) REVERT: B 380 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8350 (pp30) REVERT: B 521 MET cc_start: 0.8291 (ttt) cc_final: 0.7941 (tpt) REVERT: B 674 SER cc_start: 0.8939 (t) cc_final: 0.8647 (p) REVERT: B 705 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.8044 (m-80) outliers start: 61 outliers final: 40 residues processed: 266 average time/residue: 0.2172 time to fit residues: 85.0933 Evaluate side-chains 268 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 100 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 489 TRP Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 695 PHE Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 98 optimal weight: 0.0870 chunk 101 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.132955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108560 restraints weight = 30190.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111351 restraints weight = 16583.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113127 restraints weight = 10989.366| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10414 Z= 0.146 Angle : 0.761 11.621 14068 Z= 0.368 Chirality : 0.045 0.260 1639 Planarity : 0.005 0.059 1687 Dihedral : 12.974 161.220 1602 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.83 % Allowed : 29.35 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1247 helix: 0.58 (0.17), residues: 950 sheet: None (None), residues: 0 loop : -2.09 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 460 HIS 0.003 0.001 HIS A 658 PHE 0.032 0.002 PHE A 367 TYR 0.047 0.001 TYR A 458 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 649) hydrogen bonds : angle 5.24060 ( 1947) covalent geometry : bond 0.00331 (10414) covalent geometry : angle 0.76108 (14068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TRP cc_start: 0.5371 (OUTLIER) cc_final: 0.4199 (m-10) REVERT: A 151 TYR cc_start: 0.8505 (t80) cc_final: 0.8185 (t80) REVERT: A 179 MET cc_start: 0.7420 (mmm) cc_final: 0.7163 (mmm) REVERT: A 219 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7056 (mm) REVERT: A 264 MET cc_start: 0.7307 (mtm) cc_final: 0.7060 (mtm) REVERT: A 318 PHE cc_start: 0.8082 (t80) cc_final: 0.7850 (t80) REVERT: A 413 MET cc_start: 0.6936 (mtt) cc_final: 0.6378 (mpp) REVERT: A 447 PHE cc_start: 0.7492 (p90) cc_final: 0.7179 (p90) REVERT: A 459 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8885 (mm) REVERT: A 471 LEU cc_start: 0.3893 (OUTLIER) cc_final: 0.3519 (mm) REVERT: A 657 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7579 (mtt180) REVERT: A 797 SER cc_start: 0.4307 (OUTLIER) cc_final: 0.3812 (p) REVERT: B 178 MET cc_start: 0.8352 (mmm) cc_final: 0.7550 (ttt) REVERT: B 380 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8351 (pp30) REVERT: B 505 HIS cc_start: 0.6616 (p-80) cc_final: 0.6364 (p-80) REVERT: B 521 MET cc_start: 0.8288 (ttt) cc_final: 0.8080 (tpt) REVERT: B 674 SER cc_start: 0.8919 (t) cc_final: 0.8668 (p) REVERT: B 705 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.8061 (m-80) outliers start: 53 outliers final: 37 residues processed: 259 average time/residue: 0.1818 time to fit residues: 71.3786 Evaluate side-chains 265 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 100 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 489 TRP Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 695 PHE Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.131295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107168 restraints weight = 30487.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.109856 restraints weight = 16876.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111577 restraints weight = 11282.120| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10414 Z= 0.172 Angle : 0.803 12.241 14068 Z= 0.386 Chirality : 0.046 0.324 1639 Planarity : 0.005 0.059 1687 Dihedral : 13.016 150.863 1602 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.01 % Allowed : 29.44 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1247 helix: 0.51 (0.17), residues: 949 sheet: None (None), residues: 0 loop : -2.10 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 789 HIS 0.002 0.001 HIS A 412 PHE 0.035 0.002 PHE A 367 TYR 0.047 0.002 TYR A 458 ARG 0.003 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 649) hydrogen bonds : angle 5.36824 ( 1947) covalent geometry : bond 0.00398 (10414) covalent geometry : angle 0.80270 (14068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 TRP cc_start: 0.5211 (OUTLIER) cc_final: 0.4132 (m-10) REVERT: A 151 TYR cc_start: 0.8519 (t80) cc_final: 0.8233 (t80) REVERT: A 179 MET cc_start: 0.7490 (mmm) cc_final: 0.7222 (mmm) REVERT: A 219 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7255 (mt) REVERT: A 318 PHE cc_start: 0.8016 (t80) cc_final: 0.7769 (t80) REVERT: A 413 MET cc_start: 0.6859 (mtt) cc_final: 0.6316 (mpp) REVERT: A 447 PHE cc_start: 0.7504 (p90) cc_final: 0.7246 (p90) REVERT: A 459 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8900 (mm) REVERT: A 797 SER cc_start: 0.4175 (OUTLIER) cc_final: 0.3667 (p) REVERT: B 178 MET cc_start: 0.8309 (mmm) cc_final: 0.7538 (ttt) REVERT: B 299 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6890 (tp30) REVERT: B 380 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8357 (pp30) REVERT: B 521 MET cc_start: 0.8332 (ttt) cc_final: 0.8088 (tpt) REVERT: B 674 SER cc_start: 0.8949 (t) cc_final: 0.8702 (p) REVERT: B 705 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8163 (m-80) outliers start: 55 outliers final: 45 residues processed: 253 average time/residue: 0.1951 time to fit residues: 75.0405 Evaluate side-chains 271 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 100 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 489 TRP Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 695 PHE Chi-restraints excluded: chain B residue 696 CYS Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.2464 > 50: distance: 26 - 48: 21.714 distance: 30 - 36: 32.381 distance: 31 - 56: 25.529 distance: 36 - 37: 47.664 distance: 37 - 38: 56.129 distance: 37 - 40: 39.816 distance: 38 - 39: 55.873 distance: 38 - 44: 42.106 distance: 39 - 67: 39.524 distance: 40 - 41: 15.764 distance: 40 - 42: 40.240 distance: 41 - 43: 10.638 distance: 44 - 45: 51.239 distance: 45 - 46: 47.315 distance: 46 - 47: 8.233 distance: 46 - 48: 30.761 distance: 47 - 72: 43.492 distance: 48 - 49: 14.785 distance: 49 - 50: 12.331 distance: 49 - 52: 17.432 distance: 50 - 51: 27.636 distance: 50 - 56: 40.298 distance: 51 - 80: 25.669 distance: 52 - 53: 46.790 distance: 53 - 54: 10.770 distance: 53 - 55: 45.251 distance: 56 - 57: 12.136 distance: 57 - 58: 18.415 distance: 57 - 60: 16.801 distance: 58 - 59: 23.441 distance: 58 - 67: 30.626 distance: 59 - 88: 30.476 distance: 60 - 61: 16.493 distance: 61 - 62: 13.391 distance: 61 - 63: 20.536 distance: 62 - 64: 7.875 distance: 63 - 65: 20.743 distance: 64 - 66: 13.768 distance: 65 - 66: 13.589 distance: 67 - 68: 3.672 distance: 68 - 69: 33.688 distance: 68 - 71: 23.358 distance: 69 - 70: 14.355 distance: 69 - 72: 23.269 distance: 70 - 94: 25.134 distance: 72 - 73: 17.662 distance: 73 - 74: 20.466 distance: 73 - 76: 18.204 distance: 74 - 75: 9.421 distance: 74 - 80: 36.315 distance: 75 - 100: 13.038 distance: 76 - 77: 9.647 distance: 77 - 78: 44.766 distance: 77 - 79: 8.851 distance: 80 - 81: 46.530 distance: 81 - 82: 47.981 distance: 81 - 84: 8.139 distance: 82 - 83: 18.834 distance: 82 - 88: 11.609 distance: 83 - 106: 34.900 distance: 84 - 85: 39.888 distance: 85 - 86: 40.499 distance: 85 - 87: 38.890 distance: 88 - 89: 23.703 distance: 89 - 90: 30.267 distance: 89 - 92: 7.550 distance: 90 - 94: 10.688 distance: 91 - 114: 33.407 distance: 92 - 93: 5.991 distance: 94 - 95: 14.050 distance: 95 - 96: 9.803 distance: 95 - 98: 18.519 distance: 96 - 97: 6.017 distance: 96 - 100: 27.957 distance: 97 - 121: 30.518 distance: 98 - 99: 18.508 distance: 100 - 101: 18.286 distance: 101 - 102: 11.718 distance: 101 - 104: 24.286 distance: 102 - 103: 27.189 distance: 102 - 106: 18.330 distance: 103 - 127: 19.034 distance: 104 - 105: 8.684