Starting phenix.real_space_refine on Thu Sep 18 05:03:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z90_39852/09_2025/8z90_39852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z90_39852/09_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_39852/09_2025/8z90_39852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z90_39852/09_2025/8z90_39852.map" model { file = "/net/cci-nas-00/data/ceres_data/8z90_39852/09_2025/8z90_39852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z90_39852/09_2025/8z90_39852.cif" } 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-2.0-5805/lib/python3.9/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: 3.60, per 1000 atoms: 0.27 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: 1.11 Conformation dependent library (CDL) restraints added in 642.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.96 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: 2.57 Time building geometry restraints manager: 1.52 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- 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= 0.143 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 : 10.80 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 aren 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 covalent geometry : bond 0.00290 (13853) covalent geometry : angle 0.66602 (18930) hydrogen bonds : bond 0.18644 ( 588) hydrogen bonds : angle 6.87606 ( 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 : 0.532 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: 0.8310 time to fit residues: 232.1833 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 : 0.547 ------------------------------------------------------------------------------- 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... 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 429 ASN B 650 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.091093 restraints weight = 20532.922| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.93 r_work: 0.3058 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13853 Z= 0.183 Angle : 0.638 9.053 18930 Z= 0.333 Chirality : 0.044 0.206 2123 Planarity : 0.006 0.063 2301 Dihedral : 13.889 164.533 2293 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.55 % Allowed : 9.75 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.21), residues: 1569 helix: 0.83 (0.21), residues: 683 sheet: -0.70 (0.38), residues: 181 loop : -1.31 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 92 TYR 0.014 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 covalent geometry : bond 0.00423 (13853) covalent geometry : angle 0.63795 (18930) hydrogen bonds : bond 0.04458 ( 588) hydrogen bonds : angle 4.90581 ( 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 207 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8603 (p) cc_final: 0.8167 (m) REVERT: A 133 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 149 LEU cc_start: 0.9093 (mp) cc_final: 0.8872 (mp) REVERT: B 603 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.7026 (pt0) REVERT: B 673 GLU cc_start: 0.8401 (mp0) cc_final: 0.8201 (mp0) REVERT: B 686 ARG cc_start: 0.8547 (mmp80) cc_final: 0.8324 (mmp80) REVERT: B 689 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 701 ARG cc_start: 0.7909 (mmp80) cc_final: 0.7273 (mmp80) REVERT: B 704 ARG cc_start: 0.8791 (ttt90) cc_final: 0.8357 (mtp85) REVERT: C 146 MET cc_start: 0.8265 (mmp) cc_final: 0.8006 (mpm) REVERT: C 186 ARG cc_start: 0.9141 (mtm180) cc_final: 0.8722 (mtp180) outliers start: 22 outliers final: 8 residues processed: 196 average time/residue: 0.8277 time to fit residues: 173.7631 Evaluate side-chains 178 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 134 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 149 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 148 GLN C 51 HIS C 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090750 restraints weight = 20698.120| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.93 r_work: 0.3026 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1778 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= 0.154 Angle : 0.583 6.324 18930 Z= 0.304 Chirality : 0.042 0.200 2123 Planarity : 0.005 0.056 2301 Dihedral : 13.747 165.363 2291 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.70 % Allowed : 10.60 % Favored : 87.70 % 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 aren not related in a simple way. whole: -0.28 (0.21), residues: 1569 helix: 0.99 (0.21), residues: 682 sheet: -0.53 (0.38), residues: 181 loop : -1.26 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 92 TYR 0.014 0.001 TYR B 537 PHE 0.033 0.002 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00357 (13853) covalent geometry : angle 0.58290 (18930) hydrogen bonds : bond 0.03936 ( 588) hydrogen bonds : angle 4.53980 ( 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 213 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8142 (ttm110) REVERT: A 94 VAL cc_start: 0.8635 (p) cc_final: 0.8235 (m) REVERT: A 139 GLN cc_start: 0.8560 (mm110) cc_final: 0.8278 (mm-40) REVERT: A 619 ASN cc_start: 0.8587 (p0) cc_final: 0.8378 (p0) REVERT: B 332 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9047 (mtp) REVERT: B 588 GLU cc_start: 0.7061 (pm20) cc_final: 0.6834 (pm20) REVERT: B 603 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6838 (pt0) REVERT: B 686 ARG cc_start: 0.8595 (mmp80) cc_final: 0.8357 (mmp80) REVERT: B 689 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 701 ARG cc_start: 0.7934 (mmp80) cc_final: 0.7149 (mmp80) REVERT: B 704 ARG cc_start: 0.8671 (ttt90) cc_final: 0.8345 (mtp85) REVERT: C 86 ASP cc_start: 0.8834 (t0) cc_final: 0.8626 (t0) REVERT: C 142 ARG cc_start: 0.7852 (ppt-90) cc_final: 0.7630 (mtm-85) REVERT: C 146 MET cc_start: 0.8323 (mmp) cc_final: 0.8005 (mpm) outliers start: 24 outliers final: 9 residues processed: 203 average time/residue: 0.7831 time to fit residues: 171.4677 Evaluate side-chains 171 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 374 ASP 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 131 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN C 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088577 restraints weight = 20615.639| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.93 r_work: 0.2991 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2029 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= 0.176 Angle : 0.595 6.936 18930 Z= 0.308 Chirality : 0.043 0.204 2123 Planarity : 0.005 0.053 2301 Dihedral : 13.734 164.489 2291 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.84 % Allowed : 11.73 % Favored : 86.43 % 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 aren not related in a simple way. whole: -0.18 (0.21), residues: 1569 helix: 1.05 (0.21), residues: 682 sheet: -0.49 (0.38), residues: 183 loop : -1.18 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 708 TYR 0.015 0.001 TYR B 537 PHE 0.031 0.002 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00413 (13853) covalent geometry : angle 0.59502 (18930) hydrogen bonds : bond 0.03872 ( 588) hydrogen bonds : angle 4.42555 ( 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 204 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8477 (ttm110) cc_final: 0.8225 (ttm110) REVERT: A 139 GLN cc_start: 0.8598 (mm110) cc_final: 0.8338 (mm-40) REVERT: A 619 ASN cc_start: 0.8627 (p0) cc_final: 0.8399 (p0) REVERT: B 332 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.9066 (mtp) REVERT: B 588 GLU cc_start: 0.7039 (pm20) cc_final: 0.6722 (pm20) REVERT: B 603 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6839 (pt0) REVERT: B 633 THR cc_start: 0.8766 (p) cc_final: 0.8459 (p) REVERT: B 689 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 701 ARG cc_start: 0.7946 (mmp80) cc_final: 0.7744 (mmp80) REVERT: C 69 MET cc_start: 0.9377 (ttp) cc_final: 0.8956 (ptm) REVERT: C 146 MET cc_start: 0.8340 (mmp) cc_final: 0.8024 (mpm) outliers start: 26 outliers final: 11 residues processed: 195 average time/residue: 0.8236 time to fit residues: 172.3401 Evaluate side-chains 174 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 374 ASP 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 603 GLN Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 660 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 89 optimal weight: 8.9990 chunk 128 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN B 641 GLN 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 = 0.109257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.084635 restraints weight = 21182.359| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.15 r_work: 0.2911 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2191 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= 0.125 Angle : 0.564 8.081 18930 Z= 0.292 Chirality : 0.041 0.179 2123 Planarity : 0.005 0.055 2301 Dihedral : 13.689 164.278 2291 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.91 % Allowed : 12.79 % 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 aren not related in a simple way. whole: -0.01 (0.21), residues: 1569 helix: 1.18 (0.21), residues: 682 sheet: -0.41 (0.38), residues: 173 loop : -1.07 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 196 TYR 0.014 0.001 TYR B 533 PHE 0.029 0.001 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00288 (13853) covalent geometry : angle 0.56369 (18930) hydrogen bonds : bond 0.03478 ( 588) hydrogen bonds : angle 4.31257 ( 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: 27 poor density : 175 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8240 (ttm110) REVERT: A 133 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 139 GLN cc_start: 0.8609 (mm110) cc_final: 0.8318 (mm-40) REVERT: A 156 ASN cc_start: 0.8689 (t0) cc_final: 0.8356 (t0) REVERT: A 619 ASN cc_start: 0.8626 (p0) cc_final: 0.8336 (p0) REVERT: B 332 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9039 (mtp) REVERT: B 369 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8687 (mtp) REVERT: B 588 GLU cc_start: 0.7007 (pm20) cc_final: 0.6788 (pm20) REVERT: B 603 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6851 (pt0) REVERT: B 633 THR cc_start: 0.8724 (p) cc_final: 0.8424 (p) REVERT: B 686 ARG cc_start: 0.8525 (mmp80) cc_final: 0.8138 (tpp-160) REVERT: B 689 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 701 ARG cc_start: 0.7964 (mmp80) cc_final: 0.7626 (mmp80) REVERT: C 69 MET cc_start: 0.9329 (ttp) cc_final: 0.8870 (ptm) REVERT: C 146 MET cc_start: 0.8400 (mmp) cc_final: 0.7876 (mpm) outliers start: 27 outliers final: 9 residues processed: 194 average time/residue: 0.7872 time to fit residues: 164.4021 Evaluate side-chains 178 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER 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 332 MET Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE 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 128 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.083500 restraints weight = 21112.322| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.14 r_work: 0.2870 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2332 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= 0.148 Angle : 0.582 8.673 18930 Z= 0.299 Chirality : 0.042 0.182 2123 Planarity : 0.005 0.064 2301 Dihedral : 13.677 163.969 2291 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.05 % Allowed : 13.43 % Favored : 84.52 % 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 aren not related in a simple way. whole: 0.05 (0.21), residues: 1569 helix: 1.25 (0.21), residues: 682 sheet: -0.50 (0.38), residues: 175 loop : -1.00 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 196 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 0.011 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00348 (13853) covalent geometry : angle 0.58207 (18930) hydrogen bonds : bond 0.03541 ( 588) hydrogen bonds : angle 4.26043 ( 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 202 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8072 (tp) cc_final: 0.7624 (tt) REVERT: A 139 GLN cc_start: 0.8645 (mm110) cc_final: 0.8319 (mm-40) REVERT: A 156 ASN cc_start: 0.8668 (t0) cc_final: 0.8367 (t0) REVERT: A 619 ASN cc_start: 0.8656 (p0) cc_final: 0.8355 (p0) REVERT: B 55 GLN cc_start: 0.9136 (mm110) cc_final: 0.8911 (mm-40) REVERT: B 144 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 332 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9008 (mtp) REVERT: B 588 GLU cc_start: 0.6995 (pm20) cc_final: 0.6756 (pm20) REVERT: B 603 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6757 (pt0) REVERT: B 633 THR cc_start: 0.8795 (p) cc_final: 0.8453 (p) REVERT: B 686 ARG cc_start: 0.8526 (mmp80) cc_final: 0.8147 (tpp-160) REVERT: B 689 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 701 ARG cc_start: 0.7904 (mmp80) cc_final: 0.7541 (mmp80) REVERT: B 708 ARG cc_start: 0.8798 (mmm160) cc_final: 0.8533 (tpp80) REVERT: C 69 MET cc_start: 0.9340 (ttp) cc_final: 0.8891 (ptm) REVERT: C 146 MET cc_start: 0.8414 (mmp) cc_final: 0.7859 (mpm) outliers start: 29 outliers final: 11 residues processed: 192 average time/residue: 0.7908 time to fit residues: 163.1877 Evaluate side-chains 173 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 601 VAL Chi-restraints excluded: chain B residue 603 GLN 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 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: 4.9990 chunk 111 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.109771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.085054 restraints weight = 21065.717| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.15 r_work: 0.2920 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2408 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= 0.119 Angle : 0.569 10.063 18930 Z= 0.293 Chirality : 0.041 0.176 2123 Planarity : 0.005 0.068 2301 Dihedral : 13.645 163.679 2291 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.63 % Allowed : 14.56 % Favored : 83.82 % 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 aren not related in a simple way. whole: 0.17 (0.21), residues: 1569 helix: 1.34 (0.21), residues: 682 sheet: -0.48 (0.37), residues: 175 loop : -0.92 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 196 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 0.006 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00273 (13853) covalent geometry : angle 0.56914 (18930) hydrogen bonds : bond 0.03351 ( 588) hydrogen bonds : angle 4.19607 ( 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 191 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8021 (tp) cc_final: 0.7584 (tt) REVERT: A 120 ASN cc_start: 0.8080 (p0) cc_final: 0.7541 (t0) REVERT: A 139 GLN cc_start: 0.8682 (mm110) cc_final: 0.8365 (mm-40) REVERT: A 147 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.7579 (mtm-85) REVERT: A 156 ASN cc_start: 0.8615 (t0) cc_final: 0.8294 (t0) REVERT: A 619 ASN cc_start: 0.8627 (p0) cc_final: 0.8325 (p0) REVERT: B 55 GLN cc_start: 0.9090 (mm110) cc_final: 0.8886 (mm-40) REVERT: B 144 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7901 (tm-30) REVERT: B 202 ARG cc_start: 0.8383 (ptm-80) cc_final: 0.8162 (ptm-80) REVERT: B 342 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7663 (t80) REVERT: B 633 THR cc_start: 0.8714 (p) cc_final: 0.8383 (p) REVERT: B 686 ARG cc_start: 0.8508 (mmp80) cc_final: 0.8126 (tpp-160) REVERT: B 689 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7800 (mt-10) REVERT: B 701 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7054 (mmp80) REVERT: B 704 ARG cc_start: 0.8967 (ttt90) cc_final: 0.8376 (mtp85) REVERT: B 708 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8525 (tpp80) REVERT: C 146 MET cc_start: 0.8393 (mmp) cc_final: 0.7862 (mpm) outliers start: 23 outliers final: 9 residues processed: 182 average time/residue: 0.8177 time to fit residues: 159.8966 Evaluate side-chains 172 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 PHE Chi-restraints excluded: chain B residue 359 LYS 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 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 110 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 603 GLN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.084917 restraints weight = 20875.272| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.14 r_work: 0.2921 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13853 Z= 0.129 Angle : 0.585 10.718 18930 Z= 0.300 Chirality : 0.041 0.177 2123 Planarity : 0.005 0.072 2301 Dihedral : 13.632 163.413 2291 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.48 % Allowed : 14.91 % Favored : 83.60 % 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 aren not related in a simple way. whole: 0.22 (0.21), residues: 1569 helix: 1.38 (0.21), residues: 683 sheet: -0.53 (0.36), residues: 181 loop : -0.88 (0.22), residues: 705 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 0.027 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00300 (13853) covalent geometry : angle 0.58498 (18930) hydrogen bonds : bond 0.03363 ( 588) hydrogen bonds : angle 4.17250 ( 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 187 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8028 (tp) cc_final: 0.7533 (tt) REVERT: A 139 GLN cc_start: 0.8668 (mm110) cc_final: 0.8321 (mm-40) REVERT: A 147 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: A 156 ASN cc_start: 0.8720 (t0) cc_final: 0.8420 (t0) REVERT: A 619 ASN cc_start: 0.8657 (p0) cc_final: 0.8359 (p0) REVERT: B 55 GLN cc_start: 0.9093 (mm110) cc_final: 0.8892 (mm-40) REVERT: B 144 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 202 ARG cc_start: 0.8382 (ptm-80) cc_final: 0.8129 (ptm-80) REVERT: B 342 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7604 (t80) REVERT: B 686 ARG cc_start: 0.8525 (mmp80) cc_final: 0.8146 (tpp-160) REVERT: B 689 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7794 (mt-10) REVERT: B 701 ARG cc_start: 0.7823 (mmp80) cc_final: 0.7066 (mmp80) REVERT: B 704 ARG cc_start: 0.8950 (ttt90) cc_final: 0.8158 (mtm110) REVERT: B 708 ARG cc_start: 0.8770 (mmm160) cc_final: 0.8544 (tpp80) REVERT: C 140 GLU cc_start: 0.7290 (pp20) cc_final: 0.7075 (pp20) REVERT: C 146 MET cc_start: 0.8383 (mmp) cc_final: 0.7827 (mpm) outliers start: 21 outliers final: 12 residues processed: 179 average time/residue: 0.8583 time to fit residues: 164.7860 Evaluate side-chains 172 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 PHE Chi-restraints excluded: chain B residue 359 LYS 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 699 GLU Chi-restraints excluded: chain B residue 703 LYS 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 42 optimal weight: 6.9990 chunk 128 optimal weight: 0.0770 chunk 74 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 18 optimal weight: 0.0020 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5346 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086752 restraints weight = 21000.194| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.14 r_work: 0.2953 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 13853 Z= 0.120 Angle : 0.592 11.234 18930 Z= 0.305 Chirality : 0.041 0.244 2123 Planarity : 0.005 0.080 2301 Dihedral : 13.598 163.041 2291 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.34 % Allowed : 15.12 % Favored : 83.53 % 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 aren not related in a simple way. whole: 0.31 (0.21), residues: 1569 helix: 1.45 (0.21), residues: 683 sheet: -0.47 (0.36), residues: 180 loop : -0.82 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 196 TYR 0.014 0.001 TYR B 533 PHE 0.027 0.001 PHE C 41 TRP 0.010 0.001 TRP A 336 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00278 (13853) covalent geometry : angle 0.59230 (18930) hydrogen bonds : bond 0.03262 ( 588) hydrogen bonds : angle 4.13682 ( 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 192 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.7885 (tp) cc_final: 0.7436 (tt) REVERT: A 120 ASN cc_start: 0.8087 (p0) cc_final: 0.7126 (t0) REVERT: A 139 GLN cc_start: 0.8664 (mm110) cc_final: 0.8316 (mm-40) REVERT: A 147 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7635 (mtm-85) REVERT: A 149 LEU cc_start: 0.8914 (mp) cc_final: 0.8698 (mp) REVERT: A 156 ASN cc_start: 0.8834 (t0) cc_final: 0.8552 (t0) REVERT: A 619 ASN cc_start: 0.8656 (p0) cc_final: 0.8360 (p0) REVERT: B 55 GLN cc_start: 0.9093 (mm110) cc_final: 0.8892 (mm-40) REVERT: B 144 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7954 (tm-30) REVERT: B 202 ARG cc_start: 0.8395 (ptm-80) cc_final: 0.8128 (ptm-80) REVERT: B 332 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8818 (mtp) REVERT: B 342 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7533 (t80) REVERT: B 686 ARG cc_start: 0.8527 (mmp80) cc_final: 0.8152 (tpp-160) REVERT: B 689 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 704 ARG cc_start: 0.8787 (ttt90) cc_final: 0.8383 (ptm160) REVERT: B 708 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8491 (tpp80) REVERT: C 55 MET cc_start: 0.9152 (mmt) cc_final: 0.8896 (tpp) REVERT: C 146 MET cc_start: 0.8358 (mmp) cc_final: 0.7859 (mpm) outliers start: 19 outliers final: 11 residues processed: 183 average time/residue: 0.8229 time to fit residues: 161.8934 Evaluate side-chains 170 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 342 PHE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 526 MET 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 703 LYS 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: 5.9990 chunk 157 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 120 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 overall best weight: 2.9784 ------------------------------------------------------------------------------- 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** A 63 GLN B 16 GLN C 131 GLN C 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.081319 restraints weight = 20933.666| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.11 r_work: 0.2850 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13853 Z= 0.226 Angle : 0.657 12.208 18930 Z= 0.338 Chirality : 0.045 0.242 2123 Planarity : 0.005 0.091 2301 Dihedral : 13.722 163.113 2291 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.55 % Allowed : 15.27 % Favored : 83.18 % 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 aren not related in a simple way. whole: 0.12 (0.21), residues: 1569 helix: 1.27 (0.21), residues: 689 sheet: -0.58 (0.36), residues: 180 loop : -0.91 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 196 TYR 0.018 0.002 TYR B 537 PHE 0.027 0.002 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00538 (13853) covalent geometry : angle 0.65663 (18930) hydrogen bonds : bond 0.03952 ( 588) hydrogen bonds : angle 4.27607 ( 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 191 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8060 (tp) cc_final: 0.7558 (tt) REVERT: A 120 ASN cc_start: 0.8133 (p0) cc_final: 0.7560 (t0) REVERT: A 134 ARG cc_start: 0.8596 (mtm180) cc_final: 0.8080 (mtp180) REVERT: A 139 GLN cc_start: 0.8671 (mm110) cc_final: 0.8338 (mm-40) REVERT: A 149 LEU cc_start: 0.8901 (mp) cc_final: 0.8686 (mp) REVERT: A 156 ASN cc_start: 0.8839 (t0) cc_final: 0.8575 (t0) REVERT: A 196 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7869 (mmm160) REVERT: A 584 GLN cc_start: 0.8774 (mp10) cc_final: 0.8511 (mm110) REVERT: A 619 ASN cc_start: 0.8739 (p0) cc_final: 0.8455 (p0) REVERT: B 55 GLN cc_start: 0.9118 (mm110) cc_final: 0.8910 (mm-40) REVERT: B 144 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7909 (tm-30) REVERT: B 689 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 704 ARG cc_start: 0.8922 (ttt90) cc_final: 0.8377 (ptm160) REVERT: B 708 ARG cc_start: 0.8754 (mmm160) cc_final: 0.8507 (tpp80) REVERT: C 140 GLU cc_start: 0.7331 (pp20) cc_final: 0.7029 (pp20) REVERT: C 146 MET cc_start: 0.8409 (mmp) cc_final: 0.7800 (mpm) outliers start: 22 outliers final: 11 residues processed: 180 average time/residue: 0.8363 time to fit residues: 161.6521 Evaluate side-chains 171 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 703 LYS 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 121 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 113 GLN C 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.084194 restraints weight = 20966.804| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.14 r_work: 0.2903 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2691 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= 0.134 Angle : 0.610 11.964 18930 Z= 0.312 Chirality : 0.042 0.221 2123 Planarity : 0.005 0.078 2301 Dihedral : 13.650 162.839 2291 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.85 % Allowed : 16.04 % Favored : 83.11 % 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 aren not related in a simple way. whole: 0.21 (0.21), residues: 1569 helix: 1.33 (0.21), residues: 689 sheet: -0.46 (0.36), residues: 179 loop : -0.87 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 196 TYR 0.015 0.001 TYR C 250 PHE 0.028 0.001 PHE C 41 TRP 0.011 0.001 TRP A 336 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00311 (13853) covalent geometry : angle 0.60968 (18930) hydrogen bonds : bond 0.03422 ( 588) hydrogen bonds : angle 4.19145 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5220.28 seconds wall clock time: 89 minutes 52.39 seconds (5392.39 seconds total)