Starting phenix.real_space_refine on Fri Jul 3 12:50:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z90_39852/07_2026/8z90_39852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z90_39852/07_2026/8z90_39852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z90_39852/07_2026/8z90_39852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z90_39852/07_2026/8z90_39852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z90_39852/07_2026/8z90_39852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z90_39852/07_2026/8z90_39852.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. 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 36 5.49 5 S 77 5.16 5 C 8402 2.51 5 N 2345 2.21 5 O 2621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13481 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5014 Classifications: {'peptide': 620} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 588} Chain: "B" Number of atoms: 5710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5710 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 39, 'TRANS': 670} Chain: "C" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1986 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 16, 'TRANS': 228} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.20 Number of scatterers: 13481 At special positions: 0 Unit cell: (103.323, 106.018, 137.465, 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 77 16.00 P 36 15.00 O 2621 8.00 N 2345 7.00 C 8402 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: 0.86 Conformation dependent library (CDL) restraints added in 469.4 milliseconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3006 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 48.9% alpha, 10.5% beta 8 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.665A pdb=" N THR A 24 " --> pdb=" O ASP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.515A pdb=" N ASP A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 154 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.553A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 335 through 344 removed outlier: 4.122A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.505A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.596A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.601A pdb=" N ASN A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.553A pdb=" N ILE A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.590A pdb=" N ARG A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.760A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.640A pdb=" N THR B 5 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 removed outlier: 4.271A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.545A pdb=" N ILE B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.579A pdb=" N LYS B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.681A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.544A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.606A pdb=" N LYS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.727A pdb=" N LEU B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.661A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.599A pdb=" N MET B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 373 through 378 removed outlier: 3.705A pdb=" N VAL B 377 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.730A pdb=" N VAL B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.517A pdb=" N THR B 485 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 647 through 662 Processing helix chain 'B' and resid 679 through 695 Processing helix chain 'B' and resid 698 through 709 removed outlier: 3.601A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 36 removed outlier: 6.674A pdb=" N THR C 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.783A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.587A pdb=" N VAL C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.888A pdb=" N GLN C 173 " --> pdb=" O HIS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 192 through 201 removed outlier: 3.573A pdb=" N LEU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.673A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.745A pdb=" N CYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.590A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 5.358A pdb=" N PHE A 425 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 416 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 427 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.972A pdb=" N LEU B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 531 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AB2, first strand: chain 'B' and resid 188 through 191 removed outlier: 3.948A pdb=" N GLN B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 246 removed outlier: 6.954A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB5, first strand: chain 'B' and resid 608 through 611 Processing sheet with id=AB6, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.619A pdb=" N ILE C 67 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG C 98 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.542A pdb=" N ARG C 142 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.743A pdb=" N LYS C 151 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 227 " --> pdb=" O LYS C 151 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4319 1.34 - 1.47: 3350 1.47 - 1.60: 6019 1.60 - 1.72: 37 1.72 - 1.85: 128 Bond restraints: 13853 Sorted by residual: bond pdb=" CB PRO A 55 " pdb=" CG PRO A 55 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.32e+00 bond pdb=" CA ARG B 323 " pdb=" C ARG B 323 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.40e-02 5.10e+03 2.53e+00 bond pdb=" C ARG B 96 " pdb=" N PRO B 97 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.98e+00 bond pdb=" C ILE C 167 " pdb=" N PRO C 168 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.65e+00 bond pdb=" C3' A E 2 " pdb=" O3' A E 2 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.50e+00 ... (remaining 13848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 18243 1.56 - 3.11: 570 3.11 - 4.67: 99 4.67 - 6.22: 14 6.22 - 7.78: 4 Bond angle restraints: 18930 Sorted by residual: angle pdb=" CA PRO A 55 " pdb=" N PRO A 55 " pdb=" CD PRO A 55 " ideal model delta sigma weight residual 112.00 105.50 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" N SER A 616 " pdb=" CA SER A 616 " pdb=" C SER A 616 " ideal model delta sigma weight residual 114.09 107.18 6.91 1.55e+00 4.16e-01 1.99e+01 angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 111.48 107.72 3.76 9.40e-01 1.13e+00 1.60e+01 angle pdb=" N VAL B 669 " pdb=" CA VAL B 669 " pdb=" C VAL B 669 " ideal model delta sigma weight residual 112.83 108.96 3.87 9.90e-01 1.02e+00 1.53e+01 angle pdb=" C THR C 40 " pdb=" N PHE C 41 " pdb=" CA PHE C 41 " ideal model delta sigma weight residual 122.65 116.46 6.19 1.60e+00 3.91e-01 1.50e+01 ... (remaining 18925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 8316 34.36 - 68.71: 181 68.71 - 103.07: 21 103.07 - 137.43: 1 137.43 - 171.79: 2 Dihedral angle restraints: 8521 sinusoidal: 3892 harmonic: 4629 Sorted by residual: dihedral pdb=" CA MET A 538 " pdb=" C MET A 538 " pdb=" N THR A 539 " pdb=" CA THR A 539 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA HIS C 233 " pdb=" C HIS C 233 " pdb=" N THR C 234 " pdb=" CA THR C 234 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sinusoidal sigma weight residual -110.00 61.79 -171.79 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1561 0.043 - 0.086: 441 0.086 - 0.129: 107 0.129 - 0.172: 12 0.172 - 0.215: 2 Chirality restraints: 2123 Sorted by residual: chirality pdb=" CB VAL A 132 " pdb=" CA VAL A 132 " pdb=" CG1 VAL A 132 " pdb=" CG2 VAL A 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' A E 2 " pdb=" C4' A E 2 " pdb=" O3' A E 2 " pdb=" C2' A E 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" C3' C E 7 " pdb=" C4' C E 7 " pdb=" O3' C E 7 " pdb=" C2' C E 7 " both_signs ideal model delta sigma weight residual False -2.48 -2.33 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 2120 not shown) Planarity restraints: 2301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 54 " -0.067 5.00e-02 4.00e+02 9.89e-02 1.56e+01 pdb=" N PRO A 55 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 643 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO B 644 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO B 97 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.039 5.00e-02 4.00e+02 ... (remaining 2298 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 294 2.67 - 3.23: 13017 3.23 - 3.79: 21822 3.79 - 4.34: 31033 4.34 - 4.90: 49500 Nonbonded interactions: 115666 Sorted by model distance: nonbonded pdb=" OD1 ASN B 306 " pdb=" O2' G2P B 801 " model vdw 2.113 3.040 nonbonded pdb=" OG SER A 318 " pdb=" OE1 GLU A 320 " model vdw 2.138 3.040 nonbonded pdb=" OD2 ASP A 21 " pdb=" OG1 THR A 24 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR C 229 " pdb=" O VAL C 231 " model vdw 2.188 3.040 nonbonded pdb=" O ALA B 404 " pdb=" OG SER B 407 " model vdw 2.211 3.040 ... (remaining 115661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 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 : 0.003 0.091 13853 Z= 0.146 Angle : 0.666 7.780 18930 Z= 0.401 Chirality : 0.042 0.215 2123 Planarity : 0.006 0.099 2301 Dihedral : 14.444 171.787 5515 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1569 helix: 0.55 (0.21), residues: 678 sheet: -0.86 (0.38), residues: 180 loop : -1.37 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 96 TYR 0.018 0.001 TYR A 96 PHE 0.034 0.002 PHE C 149 TRP 0.014 0.001 TRP A 13 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (13853) covalent geometry : angle 0.66603 / 0.40 (18930) hydrogen bonds : bond 0.18644 / 12.51 ( 588) hydrogen bonds : angle 6.87606 / 4.88 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.9008 (mp) cc_final: 0.8800 (mp) REVERT: B 167 ASP cc_start: 0.7999 (m-30) cc_final: 0.7713 (m-30) REVERT: B 673 GLU cc_start: 0.7688 (mp0) cc_final: 0.7462 (mp0) REVERT: B 701 ARG cc_start: 0.7909 (mmp80) cc_final: 0.7173 (mmp80) REVERT: B 704 ARG cc_start: 0.8443 (ttt90) cc_final: 0.8133 (mtp85) REVERT: C 146 MET cc_start: 0.7917 (mmp) cc_final: 0.7645 (mpm) outliers start: 0 outliers final: 1 residues processed: 261 average time/residue: 0.6476 time to fit residues: 181.4228 Evaluate side-chains 181 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 424 GLN A 535 GLN B 429 ASN B 650 ASN C 51 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091637 restraints weight = 20506.214| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.93 r_work: 0.3068 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13853 Z= 0.182 Angle : 0.643 8.201 18930 Z= 0.336 Chirality : 0.044 0.285 2123 Planarity : 0.006 0.060 2301 Dihedral : 13.938 164.072 2293 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.63 % Allowed : 9.75 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1569 helix: 0.78 (0.21), residues: 682 sheet: -0.70 (0.38), residues: 181 loop : -1.33 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 92 TYR 0.017 0.002 TYR B 537 PHE 0.037 0.002 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (13853) covalent geometry : angle 0.64257 / 0.34 (18930) hydrogen bonds : bond 0.04656 / 3.18 ( 588) hydrogen bonds : angle 4.96962 / 3.54 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8698 (p) cc_final: 0.8276 (m) REVERT: A 149 LEU cc_start: 0.9113 (mp) cc_final: 0.8903 (mp) REVERT: B 588 GLU cc_start: 0.7096 (pm20) cc_final: 0.6883 (pm20) REVERT: B 673 GLU cc_start: 0.8389 (mp0) cc_final: 0.8181 (mp0) REVERT: B 689 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 701 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7307 (mmp80) REVERT: B 704 ARG cc_start: 0.8824 (ttt90) cc_final: 0.8422 (mtp85) REVERT: C 146 MET cc_start: 0.8246 (mmp) cc_final: 0.8033 (mpm) REVERT: C 186 ARG cc_start: 0.9143 (mtm180) cc_final: 0.8706 (mtp180) outliers start: 23 outliers final: 8 residues processed: 199 average time/residue: 0.6669 time to fit residues: 142.5359 Evaluate side-chains 176 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 0.0770 chunk 149 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.8818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093325 restraints weight = 20566.723| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.93 r_work: 0.3091 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13853 Z= 0.125 Angle : 0.572 6.671 18930 Z= 0.300 Chirality : 0.041 0.202 2123 Planarity : 0.005 0.054 2301 Dihedral : 13.780 165.381 2291 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.48 % Allowed : 11.10 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.21), residues: 1569 helix: 1.02 (0.21), residues: 682 sheet: -0.54 (0.38), residues: 181 loop : -1.25 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.014 0.001 TYR B 533 PHE 0.030 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13853) covalent geometry : angle 0.57160 / 0.30 (18930) hydrogen bonds : bond 0.03954 / 2.71 ( 588) hydrogen bonds : angle 4.62221 / 3.28 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 149 LEU cc_start: 0.9105 (mp) cc_final: 0.8868 (mp) REVERT: B 144 GLU cc_start: 0.8309 (tp30) cc_final: 0.8092 (tm-30) REVERT: B 332 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.9027 (mtp) REVERT: B 588 GLU cc_start: 0.7058 (pm20) cc_final: 0.6711 (pm20) REVERT: B 689 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 701 ARG cc_start: 0.7900 (mmp80) cc_final: 0.7243 (mmp80) REVERT: C 142 ARG cc_start: 0.7857 (ppt-90) cc_final: 0.7623 (mtm-85) REVERT: C 146 MET cc_start: 0.8314 (mmp) cc_final: 0.8006 (mpm) REVERT: C 186 ARG cc_start: 0.9121 (mtm180) cc_final: 0.8737 (mtp180) outliers start: 21 outliers final: 7 residues processed: 192 average time/residue: 0.6489 time to fit residues: 134.2952 Evaluate side-chains 172 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 620 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 131 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN C 163 ASN C 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.090290 restraints weight = 20521.359| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.97 r_work: 0.3043 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13853 Z= 0.155 Angle : 0.583 6.684 18930 Z= 0.305 Chirality : 0.042 0.183 2123 Planarity : 0.005 0.057 2301 Dihedral : 13.766 164.585 2291 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.84 % Allowed : 11.52 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1569 helix: 1.07 (0.21), residues: 683 sheet: -0.49 (0.38), residues: 181 loop : -1.21 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 92 TYR 0.015 0.001 TYR B 537 PHE 0.030 0.002 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.010 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (13853) covalent geometry : angle 0.58336 / 0.30 (18930) hydrogen bonds : bond 0.03874 / 2.66 ( 588) hydrogen bonds : angle 4.46616 / 3.17 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8372 (m170) cc_final: 0.7974 (m170) REVERT: A 94 VAL cc_start: 0.8647 (p) cc_final: 0.8238 (m) REVERT: A 619 ASN cc_start: 0.8591 (p0) cc_final: 0.8374 (p0) REVERT: B 144 GLU cc_start: 0.8309 (tp30) cc_final: 0.8099 (tm-30) REVERT: B 332 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.9060 (mtp) REVERT: B 588 GLU cc_start: 0.7087 (pm20) cc_final: 0.6856 (pm20) REVERT: B 686 ARG cc_start: 0.8500 (mmp80) cc_final: 0.8189 (mmp80) REVERT: B 689 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7890 (mt-10) REVERT: B 704 ARG cc_start: 0.8372 (mtp85) cc_final: 0.8153 (mtp-110) REVERT: C 69 MET cc_start: 0.9398 (ttp) cc_final: 0.9048 (ttp) REVERT: C 146 MET cc_start: 0.8325 (mmp) cc_final: 0.8004 (mpm) outliers start: 26 outliers final: 7 residues processed: 191 average time/residue: 0.6226 time to fit residues: 127.6527 Evaluate side-chains 173 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 89 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 145 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 49 optimal weight: 0.0670 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 603 GLN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092279 restraints weight = 20496.976| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.93 r_work: 0.3075 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13853 Z= 0.114 Angle : 0.558 7.456 18930 Z= 0.291 Chirality : 0.041 0.211 2123 Planarity : 0.005 0.059 2301 Dihedral : 13.723 164.348 2291 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.63 % Allowed : 13.07 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1569 helix: 1.15 (0.21), residues: 683 sheet: -0.47 (0.38), residues: 184 loop : -1.09 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 92 TYR 0.014 0.001 TYR B 533 PHE 0.028 0.001 PHE C 41 TRP 0.010 0.001 TRP A 614 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (13853) covalent geometry : angle 0.55769 / 0.29 (18930) hydrogen bonds : bond 0.03541 / 2.43 ( 588) hydrogen bonds : angle 4.36307 / 3.09 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8082 (m170) cc_final: 0.7637 (m-70) REVERT: A 94 VAL cc_start: 0.8594 (p) cc_final: 0.8204 (m) REVERT: A 139 GLN cc_start: 0.8483 (mm110) cc_final: 0.8201 (mm-40) REVERT: A 619 ASN cc_start: 0.8559 (p0) cc_final: 0.8343 (p0) REVERT: B 144 GLU cc_start: 0.8295 (tp30) cc_final: 0.8088 (tm-30) REVERT: B 332 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9066 (mtp) REVERT: B 588 GLU cc_start: 0.6973 (pm20) cc_final: 0.6727 (pm20) REVERT: B 686 ARG cc_start: 0.8492 (mmp80) cc_final: 0.8212 (mmp80) REVERT: B 689 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7895 (mt-10) REVERT: C 69 MET cc_start: 0.9389 (ttp) cc_final: 0.8974 (ttp) REVERT: C 146 MET cc_start: 0.8353 (mmp) cc_final: 0.7975 (mpm) outliers start: 23 outliers final: 6 residues processed: 196 average time/residue: 0.6208 time to fit residues: 131.3797 Evaluate side-chains 177 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 100 optimal weight: 0.0970 chunk 114 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091255 restraints weight = 20509.751| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.93 r_work: 0.3035 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13853 Z= 0.139 Angle : 0.576 8.626 18930 Z= 0.299 Chirality : 0.042 0.208 2123 Planarity : 0.005 0.066 2301 Dihedral : 13.714 164.150 2291 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.84 % Allowed : 14.13 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1569 helix: 1.22 (0.21), residues: 682 sheet: -0.50 (0.38), residues: 184 loop : -1.03 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 92 TYR 0.015 0.001 TYR B 533 PHE 0.028 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13853) covalent geometry : angle 0.57643 / 0.30 (18930) hydrogen bonds : bond 0.03600 / 2.47 ( 588) hydrogen bonds : angle 4.30935 / 3.05 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8631 (p) cc_final: 0.8259 (m) REVERT: A 139 GLN cc_start: 0.8491 (mm110) cc_final: 0.8254 (mm-40) REVERT: A 149 LEU cc_start: 0.9107 (mm) cc_final: 0.8747 (mp) REVERT: A 619 ASN cc_start: 0.8590 (p0) cc_final: 0.8368 (p0) REVERT: B 144 GLU cc_start: 0.8314 (tp30) cc_final: 0.8070 (tm-30) REVERT: B 332 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9064 (mtp) REVERT: B 551 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: B 588 GLU cc_start: 0.6984 (pm20) cc_final: 0.6713 (pm20) REVERT: B 686 ARG cc_start: 0.8519 (mmp80) cc_final: 0.8267 (mmp80) REVERT: B 689 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7969 (mt-10) REVERT: C 69 MET cc_start: 0.9395 (ttp) cc_final: 0.9034 (ttp) REVERT: C 146 MET cc_start: 0.8401 (mmp) cc_final: 0.8013 (mpm) outliers start: 26 outliers final: 13 residues processed: 188 average time/residue: 0.6208 time to fit residues: 126.1402 Evaluate side-chains 178 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 82 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 GLN B 55 GLN B 641 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.083989 restraints weight = 21201.628| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.15 r_work: 0.2908 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13853 Z= 0.167 Angle : 0.592 8.885 18930 Z= 0.309 Chirality : 0.042 0.189 2123 Planarity : 0.005 0.075 2301 Dihedral : 13.720 163.987 2291 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1569 helix: 1.25 (0.21), residues: 681 sheet: -0.52 (0.38), residues: 185 loop : -1.01 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 92 TYR 0.015 0.001 TYR B 533 PHE 0.028 0.002 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (13853) covalent geometry : angle 0.59191 / 0.31 (18930) hydrogen bonds : bond 0.03707 / 2.55 ( 588) hydrogen bonds : angle 4.29279 / 3.04 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7534 (m170) cc_final: 0.7305 (m170) REVERT: A 94 VAL cc_start: 0.8498 (p) cc_final: 0.8116 (m) REVERT: A 99 LEU cc_start: 0.8119 (tp) cc_final: 0.7739 (tt) REVERT: A 120 ASN cc_start: 0.8067 (p0) cc_final: 0.7447 (t0) REVERT: A 139 GLN cc_start: 0.8582 (mm110) cc_final: 0.8311 (mm-40) REVERT: A 147 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7542 (mtm-85) REVERT: A 149 LEU cc_start: 0.8983 (mm) cc_final: 0.8627 (mp) REVERT: A 619 ASN cc_start: 0.8621 (p0) cc_final: 0.8327 (p0) REVERT: B 144 GLU cc_start: 0.8328 (tp30) cc_final: 0.8000 (tm-30) REVERT: B 332 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9051 (mtp) REVERT: B 588 GLU cc_start: 0.7042 (pm20) cc_final: 0.6785 (pm20) REVERT: B 686 ARG cc_start: 0.8509 (mmp80) cc_final: 0.8291 (mmp80) REVERT: B 689 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8013 (mt-10) REVERT: C 69 MET cc_start: 0.9345 (ttp) cc_final: 0.8864 (ptm) REVERT: C 146 MET cc_start: 0.8407 (mmp) cc_final: 0.7836 (mpm) outliers start: 25 outliers final: 12 residues processed: 178 average time/residue: 0.6704 time to fit residues: 128.5326 Evaluate side-chains 176 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 110 optimal weight: 0.0570 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.085529 restraints weight = 20848.957| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.14 r_work: 0.2923 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13853 Z= 0.126 Angle : 0.586 10.449 18930 Z= 0.304 Chirality : 0.041 0.191 2123 Planarity : 0.005 0.082 2301 Dihedral : 13.692 163.705 2291 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.41 % Allowed : 14.91 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.21), residues: 1569 helix: 1.31 (0.21), residues: 681 sheet: -0.55 (0.38), residues: 176 loop : -0.91 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 92 TYR 0.015 0.001 TYR B 533 PHE 0.027 0.001 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (13853) covalent geometry : angle 0.58585 / 0.30 (18930) hydrogen bonds : bond 0.03486 / 2.39 ( 588) hydrogen bonds : angle 4.22987 / 3.00 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7430 (m170) cc_final: 0.7140 (m170) REVERT: A 94 VAL cc_start: 0.8483 (p) cc_final: 0.8115 (m) REVERT: A 99 LEU cc_start: 0.8106 (tp) cc_final: 0.7706 (tt) REVERT: A 139 GLN cc_start: 0.8592 (mm110) cc_final: 0.8302 (mm-40) REVERT: A 147 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7629 (mtm-85) REVERT: A 149 LEU cc_start: 0.8976 (mm) cc_final: 0.8772 (mp) REVERT: A 619 ASN cc_start: 0.8613 (p0) cc_final: 0.8315 (p0) REVERT: B 144 GLU cc_start: 0.8308 (tp30) cc_final: 0.7993 (tm-30) REVERT: B 332 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9010 (mtp) REVERT: B 588 GLU cc_start: 0.6990 (pm20) cc_final: 0.6728 (pm20) REVERT: B 686 ARG cc_start: 0.8510 (mmp80) cc_final: 0.8285 (mmp80) REVERT: B 689 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 69 MET cc_start: 0.9340 (ttp) cc_final: 0.8862 (ptm) REVERT: C 140 GLU cc_start: 0.7303 (pp20) cc_final: 0.7041 (pp20) REVERT: C 146 MET cc_start: 0.8365 (mmp) cc_final: 0.7837 (mpm) outliers start: 20 outliers final: 14 residues processed: 185 average time/residue: 0.6085 time to fit residues: 121.5870 Evaluate side-chains 178 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 62 optimal weight: 0.0470 chunk 123 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN B 55 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091548 restraints weight = 20567.966| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.98 r_work: 0.3045 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13853 Z= 0.124 Angle : 0.602 10.324 18930 Z= 0.314 Chirality : 0.041 0.216 2123 Planarity : 0.006 0.091 2301 Dihedral : 13.678 163.479 2291 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.55 % Allowed : 14.98 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1569 helix: 1.39 (0.21), residues: 681 sheet: -0.57 (0.38), residues: 176 loop : -0.85 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 92 TYR 0.015 0.001 TYR B 533 PHE 0.027 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.018 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13853) covalent geometry : angle 0.60161 / 0.31 (18930) hydrogen bonds : bond 0.03479 / 2.39 ( 588) hydrogen bonds : angle 4.19472 / 2.97 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8090 (tp) cc_final: 0.7723 (tt) REVERT: A 120 ASN cc_start: 0.8084 (p0) cc_final: 0.7206 (t0) REVERT: A 139 GLN cc_start: 0.8577 (mm110) cc_final: 0.8263 (mm-40) REVERT: A 147 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: A 149 LEU cc_start: 0.9146 (mm) cc_final: 0.8913 (mp) REVERT: A 196 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7732 (mmm160) REVERT: A 619 ASN cc_start: 0.8589 (p0) cc_final: 0.8369 (p0) REVERT: B 588 GLU cc_start: 0.6967 (pm20) cc_final: 0.6752 (pm20) REVERT: B 689 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 69 MET cc_start: 0.9420 (ttp) cc_final: 0.9052 (ttp) REVERT: C 140 GLU cc_start: 0.7358 (pp20) cc_final: 0.7120 (pp20) REVERT: C 146 MET cc_start: 0.8406 (mmp) cc_final: 0.8019 (mpm) outliers start: 22 outliers final: 12 residues processed: 184 average time/residue: 0.6265 time to fit residues: 124.2992 Evaluate side-chains 169 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 26 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.084627 restraints weight = 20941.062| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.14 r_work: 0.2914 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13853 Z= 0.158 Angle : 0.625 12.558 18930 Z= 0.325 Chirality : 0.042 0.247 2123 Planarity : 0.005 0.076 2301 Dihedral : 13.677 163.371 2291 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.27 % Allowed : 15.76 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1569 helix: 1.39 (0.21), residues: 682 sheet: -0.58 (0.37), residues: 177 loop : -0.82 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 196 TYR 0.015 0.001 TYR B 533 PHE 0.028 0.002 PHE C 41 TRP 0.010 0.001 TRP A 614 HIS 0.015 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (13853) covalent geometry : angle 0.62498 / 0.32 (18930) hydrogen bonds : bond 0.03696 / 2.50 ( 588) hydrogen bonds : angle 4.17596 / 2.96 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8063 (tp) cc_final: 0.7649 (tt) REVERT: A 120 ASN cc_start: 0.8084 (p0) cc_final: 0.7176 (t0) REVERT: A 139 GLN cc_start: 0.8632 (mm110) cc_final: 0.8327 (mm-40) REVERT: A 149 LEU cc_start: 0.8975 (mm) cc_final: 0.8749 (mp) REVERT: A 263 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8279 (mp) REVERT: A 619 ASN cc_start: 0.8630 (p0) cc_final: 0.8356 (p0) REVERT: B 588 GLU cc_start: 0.7011 (pm20) cc_final: 0.6729 (pm20) REVERT: B 686 ARG cc_start: 0.8527 (mmp80) cc_final: 0.8070 (tpp-160) REVERT: B 689 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 69 MET cc_start: 0.9349 (ttp) cc_final: 0.8915 (ptm) REVERT: C 146 MET cc_start: 0.8373 (mmp) cc_final: 0.7810 (mpm) outliers start: 18 outliers final: 10 residues processed: 177 average time/residue: 0.6428 time to fit residues: 122.6281 Evaluate side-chains 170 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 121 optimal weight: 3.9990 chunk 148 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085615 restraints weight = 20983.064| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.14 r_work: 0.2929 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13853 Z= 0.130 Angle : 0.612 11.756 18930 Z= 0.318 Chirality : 0.041 0.177 2123 Planarity : 0.005 0.092 2301 Dihedral : 13.663 163.144 2291 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.34 % Allowed : 15.76 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1569 helix: 1.40 (0.21), residues: 682 sheet: -0.53 (0.38), residues: 177 loop : -0.79 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 708 TYR 0.015 0.001 TYR B 533 PHE 0.027 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.014 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (13853) covalent geometry : angle 0.61192 / 0.32 (18930) hydrogen bonds : bond 0.03555 / 2.38 ( 588) hydrogen bonds : angle 4.15398 / 2.95 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.43 seconds wall clock time: 70 minutes 39.86 seconds (4239.86 seconds total)