Starting phenix.real_space_refine on Sun Jan 19 20:08:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z90_39852/01_2025/8z90_39852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z90_39852/01_2025/8z90_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z90_39852/01_2025/8z90_39852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z90_39852/01_2025/8z90_39852.map" model { file = "/net/cci-nas-00/data/ceres_data/8z90_39852/01_2025/8z90_39852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z90_39852/01_2025/8z90_39852.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 7.92, per 1000 atoms: 0.59 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: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.37 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: 3.97 Time building geometry restraints manager: 4.08 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.210 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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= 0.187 Angle : 0.666 7.780 18930 Z= 0.392 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 : 10.76 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 (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: -0.73 (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 TRP 0.014 0.001 TRP A 13 HIS 0.007 0.001 HIS C 233 PHE 0.034 0.002 PHE C 149 TYR 0.018 0.001 TYR A 96 ARG 0.008 0.001 ARG C 96 *********************** 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 : 1.607 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: 1.6827 time to fit residues: 471.2526 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 : 1.654 ------------------------------------------------------------------------------- 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 134 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 424 GLN A 535 GLN B 148 GLN B 429 ASN B 650 ASN C 51 HIS C 233 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.088439 restraints weight = 20528.154| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.93 r_work: 0.2989 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13853 Z= 0.369 Angle : 0.675 9.030 18930 Z= 0.351 Chirality : 0.046 0.224 2123 Planarity : 0.006 0.063 2301 Dihedral : 13.914 164.394 2293 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.84 % Allowed : 9.68 % Favored : 88.48 % 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: -0.56 (0.21), residues: 1569 helix: 0.73 (0.21), residues: 685 sheet: -0.69 (0.37), residues: 179 loop : -1.38 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 336 HIS 0.005 0.001 HIS C 233 PHE 0.039 0.002 PHE C 41 TYR 0.017 0.002 TYR B 537 ARG 0.014 0.001 ARG A 92 *********************** 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 211 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8585 (p) cc_final: 0.8129 (m) REVERT: A 133 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 149 LEU cc_start: 0.9067 (mp) cc_final: 0.8842 (mp) REVERT: B 167 ASP cc_start: 0.8583 (m-30) cc_final: 0.8284 (m-30) REVERT: B 588 GLU cc_start: 0.7027 (pm20) cc_final: 0.6820 (pm20) REVERT: B 603 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7021 (pt0) REVERT: B 689 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7958 (mt-10) REVERT: B 701 ARG cc_start: 0.7968 (mmp80) cc_final: 0.7701 (mmp80) REVERT: C 146 MET cc_start: 0.8312 (mmp) cc_final: 0.8015 (mpm) REVERT: C 186 ARG cc_start: 0.9157 (mtm180) cc_final: 0.8749 (mtp180) outliers start: 26 outliers final: 9 residues processed: 196 average time/residue: 1.7164 time to fit residues: 360.8364 Evaluate side-chains 177 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU 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 229 MET Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 706 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 7 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 136 optimal weight: 0.0010 chunk 149 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 90 ASN B 148 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 = 0.3546 r_free = 0.3546 target = 0.114931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091625 restraints weight = 20436.621| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.97 r_work: 0.3051 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1751 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= 0.165 Angle : 0.567 6.391 18930 Z= 0.296 Chirality : 0.041 0.186 2123 Planarity : 0.005 0.057 2301 Dihedral : 13.748 165.355 2291 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.70 % Allowed : 11.10 % Favored : 87.21 % 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: -0.27 (0.21), residues: 1569 helix: 0.98 (0.21), residues: 683 sheet: -0.53 (0.38), residues: 181 loop : -1.24 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS A 49 PHE 0.031 0.001 PHE C 41 TYR 0.014 0.001 TYR B 533 ARG 0.012 0.001 ARG A 92 *********************** 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 215 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8148 (ttm110) REVERT: A 139 GLN cc_start: 0.8486 (mm110) cc_final: 0.8221 (mm-40) REVERT: A 156 ASN cc_start: 0.8776 (t0) cc_final: 0.8490 (t0) REVERT: A 393 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8944 (mp) REVERT: B 144 GLU cc_start: 0.8349 (tp30) cc_final: 0.8149 (tm-30) REVERT: B 332 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9047 (mtp) REVERT: B 588 GLU cc_start: 0.7076 (pm20) cc_final: 0.6714 (pm20) REVERT: B 603 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6904 (pt0) REVERT: B 689 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 701 ARG cc_start: 0.7953 (mmp80) cc_final: 0.7301 (mmp80) REVERT: B 704 ARG cc_start: 0.8665 (ttt90) cc_final: 0.8436 (mtp85) REVERT: C 142 ARG cc_start: 0.7843 (ppt-90) cc_final: 0.7622 (mtm-85) REVERT: C 146 MET cc_start: 0.8282 (mmp) cc_final: 0.8006 (mpm) outliers start: 24 outliers final: 8 residues processed: 205 average time/residue: 1.5906 time to fit residues: 352.1380 Evaluate side-chains 177 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 393 ILE 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 408 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090032 restraints weight = 20398.102| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.96 r_work: 0.3048 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1958 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= 0.213 Angle : 0.573 7.264 18930 Z= 0.296 Chirality : 0.042 0.181 2123 Planarity : 0.005 0.051 2301 Dihedral : 13.716 164.616 2291 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.84 % Allowed : 11.38 % Favored : 86.78 % 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 (0.21), residues: 1569 helix: 1.08 (0.21), residues: 682 sheet: -0.40 (0.38), residues: 181 loop : -1.16 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS C 233 PHE 0.029 0.002 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.011 0.001 ARG B 708 *********************** 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 204 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8447 (ttm110) cc_final: 0.8193 (ttm110) REVERT: A 139 GLN cc_start: 0.8543 (mm110) cc_final: 0.8275 (mm-40) REVERT: A 156 ASN cc_start: 0.8711 (t0) cc_final: 0.8443 (t0) REVERT: A 619 ASN cc_start: 0.8599 (p0) cc_final: 0.8378 (p0) REVERT: B 144 GLU cc_start: 0.8332 (tp30) cc_final: 0.8110 (tm-30) REVERT: B 332 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9052 (mtp) REVERT: B 588 GLU cc_start: 0.6995 (pm20) cc_final: 0.6764 (pm20) REVERT: B 686 ARG cc_start: 0.8505 (mmp80) cc_final: 0.8216 (mmp80) REVERT: B 689 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 701 ARG cc_start: 0.7928 (mmp80) cc_final: 0.7707 (mmp80) REVERT: C 146 MET cc_start: 0.8311 (mmp) cc_final: 0.8045 (mpm) outliers start: 26 outliers final: 10 residues processed: 193 average time/residue: 1.6668 time to fit residues: 346.7522 Evaluate side-chains 177 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP 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 30 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN B 603 GLN B 641 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.085295 restraints weight = 21037.066| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.14 r_work: 0.2928 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2155 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= 0.186 Angle : 0.557 7.867 18930 Z= 0.288 Chirality : 0.041 0.179 2123 Planarity : 0.005 0.053 2301 Dihedral : 13.674 164.215 2291 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.05 % Allowed : 12.37 % Favored : 85.58 % 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: 0.01 (0.21), residues: 1569 helix: 1.18 (0.21), residues: 682 sheet: -0.49 (0.37), residues: 180 loop : -1.01 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS C 233 PHE 0.028 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.012 0.001 ARG A 196 *********************** 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 207 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8605 (mm110) cc_final: 0.8307 (mm-40) REVERT: A 156 ASN cc_start: 0.8751 (t0) cc_final: 0.8457 (t0) REVERT: A 619 ASN cc_start: 0.8622 (p0) cc_final: 0.8330 (p0) REVERT: B 144 GLU cc_start: 0.8332 (tp30) cc_final: 0.7981 (tm-30) REVERT: B 167 ASP cc_start: 0.8654 (m-30) cc_final: 0.8450 (m-30) REVERT: B 332 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9030 (mtp) REVERT: B 588 GLU cc_start: 0.7036 (pm20) cc_final: 0.6756 (pm20) REVERT: B 686 ARG cc_start: 0.8517 (mmp80) cc_final: 0.8231 (mmp80) REVERT: B 689 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 701 ARG cc_start: 0.7944 (mmp80) cc_final: 0.7616 (mmp80) REVERT: C 69 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9069 (ttp) REVERT: C 146 MET cc_start: 0.8396 (mmp) cc_final: 0.7860 (mpm) outliers start: 29 outliers final: 11 residues processed: 196 average time/residue: 1.6139 time to fit residues: 340.7806 Evaluate side-chains 181 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 17 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 16 GLN C 163 ASN C 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.082212 restraints weight = 21415.271| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.15 r_work: 0.2874 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13853 Z= 0.289 Angle : 0.612 8.969 18930 Z= 0.315 Chirality : 0.043 0.194 2123 Planarity : 0.005 0.066 2301 Dihedral : 13.713 163.992 2291 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.33 % Allowed : 13.29 % Favored : 84.38 % 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: 0.02 (0.21), residues: 1569 helix: 1.21 (0.21), residues: 682 sheet: -0.54 (0.37), residues: 180 loop : -1.00 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS A 49 PHE 0.029 0.002 PHE C 41 TYR 0.016 0.001 TYR B 533 ARG 0.015 0.001 ARG A 92 *********************** 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 203 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8631 (mm110) cc_final: 0.8338 (mm-40) REVERT: A 147 ARG cc_start: 0.8343 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: A 156 ASN cc_start: 0.8789 (t0) cc_final: 0.8473 (t0) REVERT: A 619 ASN cc_start: 0.8683 (p0) cc_final: 0.8389 (p0) REVERT: B 144 GLU cc_start: 0.8346 (tp30) cc_final: 0.7994 (tm-30) REVERT: B 167 ASP cc_start: 0.8722 (m-30) cc_final: 0.8501 (m-30) REVERT: B 332 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9029 (mtp) REVERT: B 588 GLU cc_start: 0.7027 (pm20) cc_final: 0.6765 (pm20) REVERT: B 686 ARG cc_start: 0.8525 (mmp80) cc_final: 0.8305 (mmp80) REVERT: B 689 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8009 (mt-10) REVERT: B 701 ARG cc_start: 0.7967 (mmp80) cc_final: 0.7703 (mmp80) REVERT: B 708 ARG cc_start: 0.8796 (mmm160) cc_final: 0.8525 (tpp80) REVERT: C 69 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9092 (ttp) REVERT: C 146 MET cc_start: 0.8415 (mmp) cc_final: 0.7872 (mpm) outliers start: 33 outliers final: 12 residues processed: 190 average time/residue: 1.6868 time to fit residues: 345.2168 Evaluate side-chains 179 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE 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 660 SER Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 69 MET 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 130 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.083932 restraints weight = 20972.988| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.13 r_work: 0.2905 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13853 Z= 0.194 Angle : 0.583 10.023 18930 Z= 0.300 Chirality : 0.041 0.183 2123 Planarity : 0.005 0.074 2301 Dihedral : 13.680 163.771 2291 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.55 % Allowed : 14.49 % Favored : 83.96 % 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: 0.13 (0.21), residues: 1569 helix: 1.28 (0.21), residues: 682 sheet: -0.47 (0.37), residues: 175 loop : -0.93 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.013 0.001 HIS A 51 PHE 0.028 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.017 0.001 ARG A 92 *********************** 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 195 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8208 (tp) cc_final: 0.7762 (tt) REVERT: A 120 ASN cc_start: 0.8017 (p0) cc_final: 0.7415 (t0) REVERT: A 139 GLN cc_start: 0.8656 (mm110) cc_final: 0.8327 (mm-40) REVERT: A 156 ASN cc_start: 0.8821 (t0) cc_final: 0.8525 (t0) REVERT: A 619 ASN cc_start: 0.8639 (p0) cc_final: 0.8330 (p0) REVERT: B 144 GLU cc_start: 0.8325 (tp30) cc_final: 0.7976 (tm-30) REVERT: B 167 ASP cc_start: 0.8743 (m-30) cc_final: 0.8512 (m-30) REVERT: B 202 ARG cc_start: 0.8363 (ptm-80) cc_final: 0.8115 (ptm-80) REVERT: B 332 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8994 (mtp) REVERT: B 588 GLU cc_start: 0.6976 (pm20) cc_final: 0.6709 (pm20) REVERT: B 686 ARG cc_start: 0.8520 (mmp80) cc_final: 0.8168 (tpp-160) REVERT: B 701 ARG cc_start: 0.7827 (mmp80) cc_final: 0.7487 (mmp80) REVERT: B 708 ARG cc_start: 0.8766 (mmm160) cc_final: 0.8527 (tpp80) REVERT: C 69 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9080 (ttp) REVERT: C 146 MET cc_start: 0.8391 (mmp) cc_final: 0.7860 (mpm) outliers start: 22 outliers final: 10 residues processed: 187 average time/residue: 1.7019 time to fit residues: 343.1654 Evaluate side-chains 174 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 LYS Chi-restraints excluded: chain B residue 408 ILE 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 C residue 69 MET 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 17 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.081814 restraints weight = 21316.588| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.14 r_work: 0.2869 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13853 Z= 0.289 Angle : 0.625 10.935 18930 Z= 0.320 Chirality : 0.043 0.195 2123 Planarity : 0.005 0.075 2301 Dihedral : 13.716 163.699 2291 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.70 % Allowed : 14.42 % Favored : 83.89 % 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: 0.07 (0.21), residues: 1569 helix: 1.23 (0.20), residues: 683 sheet: -0.52 (0.37), residues: 180 loop : -0.95 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS C 233 PHE 0.028 0.002 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.019 0.001 ARG A 196 *********************** 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 196 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8225 (tp) cc_final: 0.7701 (tt) REVERT: A 139 GLN cc_start: 0.8690 (mm110) cc_final: 0.8343 (mm-40) REVERT: A 147 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.8069 (mtm-85) REVERT: A 156 ASN cc_start: 0.8851 (t0) cc_final: 0.8571 (t0) REVERT: A 393 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8880 (mp) REVERT: A 584 GLN cc_start: 0.8699 (mp10) cc_final: 0.8473 (mm110) REVERT: A 619 ASN cc_start: 0.8714 (p0) cc_final: 0.8429 (p0) REVERT: B 144 GLU cc_start: 0.8353 (tp30) cc_final: 0.8002 (tm-30) REVERT: B 167 ASP cc_start: 0.8765 (m-30) cc_final: 0.8538 (m-30) REVERT: B 332 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8964 (mtp) REVERT: B 588 GLU cc_start: 0.6992 (pm20) cc_final: 0.6717 (pm20) REVERT: B 689 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 701 ARG cc_start: 0.7848 (mmp80) cc_final: 0.7519 (mmp80) REVERT: B 708 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8518 (tpp80) REVERT: C 69 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.9090 (ttp) REVERT: C 140 GLU cc_start: 0.7339 (pp20) cc_final: 0.7118 (pp20) REVERT: C 146 MET cc_start: 0.8434 (mmp) cc_final: 0.7874 (mpm) outliers start: 24 outliers final: 14 residues processed: 185 average time/residue: 1.7021 time to fit residues: 338.7209 Evaluate side-chains 179 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE 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 660 SER Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 35 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 6 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.084126 restraints weight = 20973.521| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.14 r_work: 0.2899 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13853 Z= 0.197 Angle : 0.614 11.440 18930 Z= 0.316 Chirality : 0.042 0.261 2123 Planarity : 0.005 0.082 2301 Dihedral : 13.671 163.392 2291 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.41 % Allowed : 15.19 % Favored : 83.39 % 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: 0.22 (0.21), residues: 1569 helix: 1.37 (0.21), residues: 682 sheet: -0.53 (0.37), residues: 181 loop : -0.87 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS C 233 PHE 0.028 0.001 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.020 0.001 ARG A 196 *********************** 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: 20 poor density : 174 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8074 (tp) cc_final: 0.7618 (tt) REVERT: A 120 ASN cc_start: 0.8098 (p0) cc_final: 0.7408 (t0) REVERT: A 139 GLN cc_start: 0.8661 (mm110) cc_final: 0.8323 (mm-40) REVERT: A 147 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7669 (mtm-85) REVERT: A 149 LEU cc_start: 0.8902 (mp) cc_final: 0.8686 (mp) REVERT: A 156 ASN cc_start: 0.8891 (t0) cc_final: 0.8624 (t0) REVERT: A 196 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7808 (mmm160) REVERT: A 584 GLN cc_start: 0.8679 (mp10) cc_final: 0.8446 (mm-40) REVERT: A 619 ASN cc_start: 0.8692 (p0) cc_final: 0.8395 (p0) REVERT: B 144 GLU cc_start: 0.8345 (tp30) cc_final: 0.8009 (tm-30) REVERT: B 167 ASP cc_start: 0.8769 (m-30) cc_final: 0.8520 (m-30) REVERT: B 202 ARG cc_start: 0.8442 (ptm-80) cc_final: 0.8197 (ptm-80) REVERT: B 588 GLU cc_start: 0.6994 (pm20) cc_final: 0.6715 (pm20) REVERT: B 686 ARG cc_start: 0.8476 (mmp80) cc_final: 0.8236 (tpm-80) REVERT: B 689 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 704 ARG cc_start: 0.8803 (ttt90) cc_final: 0.8387 (ptm160) REVERT: B 708 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8522 (tpp80) REVERT: C 69 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9064 (ttp) REVERT: C 146 MET cc_start: 0.8408 (mmp) cc_final: 0.7878 (mpm) outliers start: 20 outliers final: 11 residues processed: 189 average time/residue: 1.5949 time to fit residues: 324.5170 Evaluate side-chains 175 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain C residue 69 MET 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 155 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 117 optimal weight: 0.0000 chunk 104 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** 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 = 0.3395 r_free = 0.3395 target = 0.108112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.083392 restraints weight = 20967.122| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.12 r_work: 0.2897 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2606 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= 0.229 Angle : 0.620 12.094 18930 Z= 0.318 Chirality : 0.042 0.242 2123 Planarity : 0.005 0.074 2301 Dihedral : 13.668 163.297 2291 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.48 % Allowed : 15.48 % Favored : 83.04 % 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: 0.15 (0.21), residues: 1569 helix: 1.29 (0.20), residues: 688 sheet: -0.55 (0.36), residues: 181 loop : -0.90 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS C 233 PHE 0.028 0.002 PHE C 41 TYR 0.015 0.001 TYR B 533 ARG 0.018 0.001 ARG A 196 ********************** 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 186 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.717 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8102 (tp) cc_final: 0.7641 (tt) REVERT: A 120 ASN cc_start: 0.8055 (p0) cc_final: 0.7445 (t0) REVERT: A 139 GLN cc_start: 0.8661 (mm110) cc_final: 0.8317 (mm-40) REVERT: A 156 ASN cc_start: 0.8931 (t0) cc_final: 0.8673 (t0) REVERT: A 263 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 393 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8873 (mp) REVERT: A 619 ASN cc_start: 0.8721 (p0) cc_final: 0.8422 (p0) REVERT: B 55 GLN cc_start: 0.9138 (mm110) cc_final: 0.8935 (mm-40) REVERT: B 144 GLU cc_start: 0.8346 (tp30) cc_final: 0.8004 (tm-30) REVERT: B 167 ASP cc_start: 0.8769 (m-30) cc_final: 0.8504 (m-30) REVERT: B 202 ARG cc_start: 0.8452 (ptm-80) cc_final: 0.8198 (ptm-80) REVERT: B 588 GLU cc_start: 0.7005 (pm20) cc_final: 0.6718 (pm20) REVERT: B 686 ARG cc_start: 0.8542 (mmp80) cc_final: 0.8310 (tpm-80) REVERT: B 689 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 704 ARG cc_start: 0.8847 (ttt90) cc_final: 0.8459 (ptm160) REVERT: C 69 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.9059 (ttp) REVERT: C 140 GLU cc_start: 0.7289 (pp20) cc_final: 0.6986 (pp20) REVERT: C 146 MET cc_start: 0.8401 (mmp) cc_final: 0.7848 (mpm) outliers start: 21 outliers final: 12 residues processed: 179 average time/residue: 1.7394 time to fit residues: 335.5150 Evaluate side-chains 172 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 393 ILE Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 206 VAL 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 118 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082332 restraints weight = 21220.044| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.13 r_work: 0.2848 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13853 Z= 0.270 Angle : 0.638 11.953 18930 Z= 0.327 Chirality : 0.043 0.226 2123 Planarity : 0.005 0.083 2301 Dihedral : 13.704 163.109 2291 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.06 % Allowed : 16.25 % Favored : 82.69 % 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: 0.12 (0.21), residues: 1569 helix: 1.26 (0.20), residues: 688 sheet: -0.49 (0.37), residues: 180 loop : -0.93 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS C 233 PHE 0.028 0.002 PHE C 41 TYR 0.015 0.001 TYR C 250 ARG 0.022 0.001 ARG B 708 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9660.72 seconds wall clock time: 173 minutes 25.76 seconds (10405.76 seconds total)