Starting phenix.real_space_refine on Tue May 20 18:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tu6_41617/05_2025/8tu6_41617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tu6_41617/05_2025/8tu6_41617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tu6_41617/05_2025/8tu6_41617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tu6_41617/05_2025/8tu6_41617.map" model { file = "/net/cci-nas-00/data/ceres_data/8tu6_41617/05_2025/8tu6_41617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tu6_41617/05_2025/8tu6_41617.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 74 5.16 5 C 6474 2.51 5 N 1751 2.21 5 O 1869 1.98 5 H 10170 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20338 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 16079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 16079 Classifications: {'peptide': 981} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 935} Chain breaks: 4 Chain: "B" Number of atoms: 4259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 4259 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 4, 'TRANS': 247} Chain breaks: 1 Time building chain proxies: 9.07, per 1000 atoms: 0.45 Number of scatterers: 20338 At special positions: 0 Unit cell: (90.909, 113.022, 135.135, 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 74 16.00 O 1869 8.00 N 1751 7.00 C 6474 6.00 H 10170 1.00 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: 4.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 54.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 41 through 53 Processing helix chain 'A' and resid 54 through 62 Proline residue: A 57 - end of helix removed outlier: 4.282A pdb=" N GLN A 60 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.000A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.590A pdb=" N ARG A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 216 through 230 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.517A pdb=" N GLY A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 525 through 537 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.698A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.614A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.865A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 695 removed outlier: 4.715A pdb=" N GLN A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.215A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.698A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 Processing helix chain 'A' and resid 809 through 827 Processing helix chain 'A' and resid 856 through 862 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 912 Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 939 through 944 removed outlier: 3.625A pdb=" N LYS A 942 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 943 " --> pdb=" O HIS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 4.047A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 994 removed outlier: 3.611A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.765A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 removed outlier: 3.953A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1026 removed outlier: 3.745A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1047 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 445 through 516 removed outlier: 3.880A pdb=" N LYS B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 586 Proline residue: B 568 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 7.254A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 212 removed outlier: 5.584A pdb=" N ILE A 197 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA A 289 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.098A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.724A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.640A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA A 400 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN A 428 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AA9, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AB1, first strand: chain 'A' and resid 921 through 923 Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 336 removed outlier: 4.399A pdb=" N TYR B 334 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP B 359 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY B 336 " --> pdb=" O ASP B 359 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10137 1.03 - 1.23: 50 1.23 - 1.42: 4304 1.42 - 1.62: 5944 1.62 - 1.81: 115 Bond restraints: 20550 Sorted by residual: bond pdb=" CB PRO A 298 " pdb=" CG PRO A 298 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.88e+00 bond pdb=" N MET B 326 " pdb=" CA MET B 326 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N MET B 326 " pdb=" H MET B 326 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" CA LYS A 973 " pdb=" CB LYS A 973 " ideal model delta sigma weight residual 1.533 1.550 -0.018 1.60e-02 3.91e+03 1.21e+00 bond pdb=" CB GLU B 403 " pdb=" CG GLU B 403 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.28e-01 ... (remaining 20545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 36324 1.48 - 2.97: 756 2.97 - 4.45: 80 4.45 - 5.93: 10 5.93 - 7.42: 1 Bond angle restraints: 37171 Sorted by residual: angle pdb=" CA PRO A 298 " pdb=" N PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 112.00 106.43 5.57 1.40e+00 5.10e-01 1.58e+01 angle pdb=" CA ILE A 561 " pdb=" CB ILE A 561 " pdb=" CG1 ILE A 561 " ideal model delta sigma weight residual 110.40 115.04 -4.64 1.70e+00 3.46e-01 7.43e+00 angle pdb=" C ILE A 561 " pdb=" CA ILE A 561 " pdb=" CB ILE A 561 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.82e+00 3.02e-01 6.60e+00 angle pdb=" CB LYS A 973 " pdb=" CG LYS A 973 " pdb=" CD LYS A 973 " ideal model delta sigma weight residual 111.30 117.04 -5.74 2.30e+00 1.89e-01 6.23e+00 angle pdb=" CA LYS A 973 " pdb=" CB LYS A 973 " pdb=" CG LYS A 973 " ideal model delta sigma weight residual 114.10 118.97 -4.87 2.00e+00 2.50e-01 5.94e+00 ... (remaining 37166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 8493 17.74 - 35.48: 787 35.48 - 53.23: 246 53.23 - 70.97: 57 70.97 - 88.71: 18 Dihedral angle restraints: 9601 sinusoidal: 5294 harmonic: 4307 Sorted by residual: dihedral pdb=" CA ARG B 358 " pdb=" C ARG B 358 " pdb=" N ASP B 359 " pdb=" CA ASP B 359 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CG ARG A 93 " pdb=" CD ARG A 93 " pdb=" NE ARG A 93 " pdb=" CZ ARG A 93 " ideal model delta sinusoidal sigma weight residual 90.00 41.31 48.69 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA ARG A 808 " pdb=" C ARG A 808 " pdb=" N GLN A 809 " pdb=" CA GLN A 809 " ideal model delta harmonic sigma weight residual 180.00 163.38 16.62 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 9598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 981 0.031 - 0.061: 372 0.061 - 0.092: 93 0.092 - 0.122: 63 0.122 - 0.153: 7 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CA ILE A 921 " pdb=" N ILE A 921 " pdb=" C ILE A 921 " pdb=" CB ILE A 921 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE A 338 " pdb=" N ILE A 338 " pdb=" C ILE A 338 " pdb=" CB ILE A 338 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL A 952 " pdb=" N VAL A 952 " pdb=" C VAL A 952 " pdb=" CB VAL A 952 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1513 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 93 " 0.214 9.50e-02 1.11e+02 7.17e-02 6.08e+00 pdb=" NE ARG A 93 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 93 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 93 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 93 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 93 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 93 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG A 93 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 93 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 741 " 0.153 9.50e-02 1.11e+02 5.13e-02 3.41e+00 pdb=" NE ARG A 741 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 741 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 741 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 741 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 741 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 741 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 741 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 741 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 561 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 562 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 562 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 562 " 0.021 5.00e-02 4.00e+02 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1393 2.20 - 2.80: 42495 2.80 - 3.40: 57246 3.40 - 4.00: 74662 4.00 - 4.60: 116551 Nonbonded interactions: 292347 Sorted by model distance: nonbonded pdb=" O ASN A 345 " pdb="HD22 ASN B 564 " model vdw 1.601 2.450 nonbonded pdb=" HH TYR A 584 " pdb=" OD2 ASP A 608 " model vdw 1.613 2.450 nonbonded pdb="HH21 ARG A 612 " pdb=" OE2 GLU A 642 " model vdw 1.618 2.450 nonbonded pdb="HH12 ARG A 398 " pdb=" OD1 ASP A 434 " model vdw 1.639 2.450 nonbonded pdb=" HG SER A 405 " pdb=" O LEU A 455 " model vdw 1.640 2.450 ... (remaining 292342 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.310 Extract box with map and model: 0.850 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.580 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.004 0.098 10380 Z= 0.167 Angle : 0.591 7.415 13994 Z= 0.325 Chirality : 0.039 0.153 1516 Planarity : 0.005 0.094 1796 Dihedral : 16.954 88.712 3995 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.88 % Allowed : 20.62 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.51 (0.24), residues: 1219 helix: 0.77 (0.22), residues: 588 sheet: -0.19 (0.39), residues: 156 loop : 0.19 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 780 HIS 0.008 0.001 HIS B 450 PHE 0.011 0.001 PHE A 667 TYR 0.012 0.001 TYR A 904 ARG 0.013 0.001 ARG A 741 Details of bonding type rmsd hydrogen bonds : bond 0.17149 ( 530) hydrogen bonds : angle 6.43182 ( 1491) covalent geometry : bond 0.00393 (10380) covalent geometry : angle 0.59143 (13994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7697 (mttm) cc_final: 0.7408 (tttp) REVERT: A 288 MET cc_start: 0.7256 (ttm) cc_final: 0.6871 (ttt) REVERT: A 488 ASP cc_start: 0.7293 (t0) cc_final: 0.6768 (p0) REVERT: A 573 LYS cc_start: 0.7697 (mmmm) cc_final: 0.7337 (mmtt) REVERT: A 733 LYS cc_start: 0.8406 (ttmp) cc_final: 0.8188 (ttmt) REVERT: A 811 MET cc_start: 0.8099 (ttm) cc_final: 0.7815 (ttp) REVERT: A 979 ARG cc_start: 0.6718 (ttp80) cc_final: 0.6512 (ttt-90) REVERT: A 1010 MET cc_start: 0.8399 (mtt) cc_final: 0.8032 (mtm) REVERT: B 496 GLU cc_start: 0.8607 (tp30) cc_final: 0.8333 (tp30) REVERT: B 525 MET cc_start: 0.8595 (mtt) cc_final: 0.8389 (tmm) outliers start: 10 outliers final: 6 residues processed: 157 average time/residue: 0.6642 time to fit residues: 136.6871 Evaluate side-chains 136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 965 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN A 825 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126059 restraints weight = 35068.506| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.00 r_work: 0.3373 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10380 Z= 0.134 Angle : 0.538 5.206 13994 Z= 0.286 Chirality : 0.039 0.141 1516 Planarity : 0.004 0.063 1796 Dihedral : 5.043 55.534 1361 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.38 % Allowed : 17.36 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.83 (0.24), residues: 1219 helix: 1.12 (0.21), residues: 596 sheet: -0.25 (0.38), residues: 158 loop : 0.29 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 780 HIS 0.003 0.001 HIS A 59 PHE 0.011 0.001 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.004 0.000 ARG A 975 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 530) hydrogen bonds : angle 4.88077 ( 1491) covalent geometry : bond 0.00303 (10380) covalent geometry : angle 0.53755 (13994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.7947 (p90) cc_final: 0.7718 (p90) REVERT: A 108 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7927 (mtp-110) REVERT: A 184 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8071 (mmtt) REVERT: A 282 MET cc_start: 0.7552 (mtp) cc_final: 0.7268 (ttm) REVERT: A 288 MET cc_start: 0.7911 (ttm) cc_final: 0.7648 (ttt) REVERT: A 809 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: A 937 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8254 (p90) REVERT: A 975 ARG cc_start: 0.7447 (tmt170) cc_final: 0.7240 (tmt170) outliers start: 27 outliers final: 16 residues processed: 158 average time/residue: 0.6352 time to fit residues: 132.5837 Evaluate side-chains 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.157885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121548 restraints weight = 35213.121| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.19 r_work: 0.3315 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10380 Z= 0.221 Angle : 0.576 6.604 13994 Z= 0.303 Chirality : 0.041 0.148 1516 Planarity : 0.005 0.068 1796 Dihedral : 5.167 56.010 1359 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.91 % Allowed : 17.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.48 (0.24), residues: 1219 helix: 0.96 (0.21), residues: 595 sheet: -0.59 (0.40), residues: 149 loop : -0.03 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 780 HIS 0.005 0.001 HIS A 213 PHE 0.018 0.002 PHE A 930 TYR 0.009 0.001 TYR A1038 ARG 0.005 0.000 ARG A 808 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 530) hydrogen bonds : angle 4.70954 ( 1491) covalent geometry : bond 0.00531 (10380) covalent geometry : angle 0.57597 (13994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7280 (pp) REVERT: A 108 ARG cc_start: 0.8170 (mmm160) cc_final: 0.7963 (mtp-110) REVERT: A 184 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8021 (mmtt) REVERT: A 219 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: A 288 MET cc_start: 0.7906 (ttm) cc_final: 0.7660 (ttt) REVERT: A 448 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8603 (p) REVERT: A 561 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7943 (pt) REVERT: A 610 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8276 (mpp) outliers start: 33 outliers final: 19 residues processed: 160 average time/residue: 0.5962 time to fit residues: 129.2969 Evaluate side-chains 158 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN A 797 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.159610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124181 restraints weight = 35525.518| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.04 r_work: 0.3340 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10380 Z= 0.151 Angle : 0.518 5.566 13994 Z= 0.271 Chirality : 0.039 0.139 1516 Planarity : 0.004 0.058 1796 Dihedral : 4.913 56.851 1358 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 16.21 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.68 (0.25), residues: 1219 helix: 1.15 (0.21), residues: 599 sheet: -0.58 (0.41), residues: 149 loop : 0.05 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE A 930 TYR 0.008 0.001 TYR A 904 ARG 0.004 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 530) hydrogen bonds : angle 4.50049 ( 1491) covalent geometry : bond 0.00360 (10380) covalent geometry : angle 0.51815 (13994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7419 (m-30) cc_final: 0.6831 (t0) REVERT: A 184 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8007 (mmtt) REVERT: A 219 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: A 288 MET cc_start: 0.7905 (ttm) cc_final: 0.7662 (ttt) REVERT: A 336 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8628 (mt) REVERT: A 448 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 561 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7904 (pt) REVERT: A 809 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: A 1012 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7454 (mt-10) REVERT: B 380 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8937 (mt) REVERT: B 421 ASP cc_start: 0.7619 (t0) cc_final: 0.7064 (t0) outliers start: 36 outliers final: 22 residues processed: 173 average time/residue: 0.5732 time to fit residues: 134.6430 Evaluate side-chains 162 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN A 825 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122892 restraints weight = 35578.962| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.03 r_work: 0.3295 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10380 Z= 0.197 Angle : 0.541 5.212 13994 Z= 0.284 Chirality : 0.040 0.145 1516 Planarity : 0.005 0.063 1796 Dihedral : 4.953 55.369 1358 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.79 % Allowed : 16.48 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.55 (0.24), residues: 1219 helix: 1.08 (0.21), residues: 598 sheet: -0.71 (0.41), residues: 149 loop : -0.04 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.015 0.002 PHE A 930 TYR 0.010 0.001 TYR A1038 ARG 0.005 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 530) hydrogen bonds : angle 4.51881 ( 1491) covalent geometry : bond 0.00477 (10380) covalent geometry : angle 0.54052 (13994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7345 (pp) REVERT: A 219 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: A 288 MET cc_start: 0.7908 (ttm) cc_final: 0.7647 (ttt) REVERT: A 336 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8629 (mt) REVERT: A 448 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 561 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7887 (pt) REVERT: A 809 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: B 380 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8926 (mt) REVERT: B 421 ASP cc_start: 0.7638 (t0) cc_final: 0.7028 (t0) outliers start: 43 outliers final: 27 residues processed: 167 average time/residue: 0.5341 time to fit residues: 125.1251 Evaluate side-chains 167 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 114 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 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 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.159540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122596 restraints weight = 35395.754| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.99 r_work: 0.3319 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10380 Z= 0.142 Angle : 0.504 5.150 13994 Z= 0.263 Chirality : 0.038 0.140 1516 Planarity : 0.004 0.053 1796 Dihedral : 4.802 55.614 1358 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.17 % Allowed : 17.00 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.75 (0.25), residues: 1219 helix: 1.30 (0.21), residues: 597 sheet: -0.70 (0.41), residues: 149 loop : 0.03 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.011 0.001 PHE A 930 TYR 0.010 0.001 TYR A 265 ARG 0.008 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 530) hydrogen bonds : angle 4.37566 ( 1491) covalent geometry : bond 0.00339 (10380) covalent geometry : angle 0.50429 (13994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7361 (pp) REVERT: A 219 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: A 288 MET cc_start: 0.7968 (ttm) cc_final: 0.7714 (ttt) REVERT: A 336 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8632 (mt) REVERT: A 561 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7878 (pt) REVERT: A 796 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 809 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: A 973 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8281 (mmtp) REVERT: B 380 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8929 (mt) REVERT: B 421 ASP cc_start: 0.7663 (t0) cc_final: 0.6982 (t0) outliers start: 36 outliers final: 23 residues processed: 164 average time/residue: 0.5544 time to fit residues: 123.6292 Evaluate side-chains 167 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122866 restraints weight = 35409.066| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.00 r_work: 0.3326 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10380 Z= 0.136 Angle : 0.494 5.115 13994 Z= 0.258 Chirality : 0.038 0.140 1516 Planarity : 0.004 0.056 1796 Dihedral : 4.727 55.078 1358 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.91 % Allowed : 17.36 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.82 (0.25), residues: 1219 helix: 1.37 (0.21), residues: 599 sheet: -0.71 (0.41), residues: 149 loop : 0.05 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 PHE 0.011 0.001 PHE A 930 TYR 0.011 0.001 TYR A 265 ARG 0.008 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 530) hydrogen bonds : angle 4.31219 ( 1491) covalent geometry : bond 0.00325 (10380) covalent geometry : angle 0.49408 (13994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7373 (pp) REVERT: A 219 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: A 288 MET cc_start: 0.7989 (ttm) cc_final: 0.7726 (ttt) REVERT: A 336 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8626 (mt) REVERT: A 448 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8598 (p) REVERT: A 561 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7882 (pt) REVERT: A 796 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 809 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: A 825 GLN cc_start: 0.7547 (mm110) cc_final: 0.7303 (mm-40) REVERT: A 973 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8276 (mmtp) REVERT: B 380 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8919 (mt) REVERT: B 421 ASP cc_start: 0.7747 (t0) cc_final: 0.7069 (t0) outliers start: 33 outliers final: 22 residues processed: 161 average time/residue: 0.5427 time to fit residues: 121.0274 Evaluate side-chains 160 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 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 = 0.3929 r_free = 0.3929 target = 0.159531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122896 restraints weight = 35283.887| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.97 r_work: 0.3334 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10380 Z= 0.131 Angle : 0.489 5.080 13994 Z= 0.256 Chirality : 0.038 0.139 1516 Planarity : 0.004 0.059 1796 Dihedral : 4.641 54.625 1358 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.56 % Allowed : 17.89 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.94 (0.25), residues: 1219 helix: 1.45 (0.21), residues: 597 sheet: -0.66 (0.41), residues: 149 loop : 0.14 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 PHE 0.010 0.001 PHE A 930 TYR 0.011 0.001 TYR A 265 ARG 0.008 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 530) hydrogen bonds : angle 4.26070 ( 1491) covalent geometry : bond 0.00314 (10380) covalent geometry : angle 0.48936 (13994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7362 (pp) REVERT: A 219 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: A 288 MET cc_start: 0.7957 (ttm) cc_final: 0.7695 (ttt) REVERT: A 336 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8626 (mt) REVERT: A 561 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7873 (pt) REVERT: A 796 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7018 (p0) REVERT: A 809 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: A 973 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8308 (mmtp) REVERT: B 380 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8889 (mt) REVERT: B 421 ASP cc_start: 0.7789 (t0) cc_final: 0.7101 (t0) outliers start: 29 outliers final: 19 residues processed: 154 average time/residue: 0.5268 time to fit residues: 112.8351 Evaluate side-chains 155 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123522 restraints weight = 35413.774| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.07 r_work: 0.3331 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10380 Z= 0.121 Angle : 0.480 5.051 13994 Z= 0.251 Chirality : 0.038 0.137 1516 Planarity : 0.004 0.059 1796 Dihedral : 4.535 54.665 1357 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.73 % Allowed : 17.44 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 0.99 (0.25), residues: 1219 helix: 1.50 (0.21), residues: 602 sheet: -0.66 (0.42), residues: 149 loop : 0.15 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 PHE 0.010 0.001 PHE A 930 TYR 0.014 0.001 TYR A 265 ARG 0.009 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 530) hydrogen bonds : angle 4.21129 ( 1491) covalent geometry : bond 0.00290 (10380) covalent geometry : angle 0.48018 (13994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7378 (pp) REVERT: A 219 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: A 288 MET cc_start: 0.7954 (ttm) cc_final: 0.7695 (ttt) REVERT: A 336 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8623 (mt) REVERT: A 561 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7865 (pt) REVERT: A 675 MET cc_start: 0.8210 (tpp) cc_final: 0.7944 (tpp) REVERT: A 796 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.6974 (p0) REVERT: A 809 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: A 973 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8384 (mmtp) REVERT: B 380 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8880 (mt) REVERT: B 421 ASP cc_start: 0.7828 (t0) cc_final: 0.7162 (t0) outliers start: 31 outliers final: 21 residues processed: 147 average time/residue: 0.5314 time to fit residues: 108.7484 Evaluate side-chains 152 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.159431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123909 restraints weight = 35384.950| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.06 r_work: 0.3338 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10380 Z= 0.118 Angle : 0.480 5.050 13994 Z= 0.250 Chirality : 0.038 0.136 1516 Planarity : 0.004 0.061 1796 Dihedral : 4.466 54.346 1357 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.38 % Allowed : 17.62 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1219 helix: 1.58 (0.21), residues: 602 sheet: -0.63 (0.42), residues: 149 loop : 0.19 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 780 HIS 0.004 0.001 HIS A 940 PHE 0.009 0.001 PHE A 930 TYR 0.011 0.001 TYR A 265 ARG 0.009 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 530) hydrogen bonds : angle 4.17339 ( 1491) covalent geometry : bond 0.00281 (10380) covalent geometry : angle 0.47951 (13994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7382 (pp) REVERT: A 336 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8605 (mt) REVERT: A 561 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7859 (pt) REVERT: A 675 MET cc_start: 0.8207 (tpp) cc_final: 0.7944 (tpp) REVERT: A 796 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.6964 (p0) REVERT: A 809 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: A 973 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8383 (mmtp) REVERT: A 1012 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 380 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8854 (mt) REVERT: B 421 ASP cc_start: 0.7867 (t0) cc_final: 0.7200 (t0) outliers start: 27 outliers final: 20 residues processed: 149 average time/residue: 0.5351 time to fit residues: 110.2940 Evaluate side-chains 152 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 296 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 809 GLN Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 563 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.159467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124949 restraints weight = 35525.766| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.03 r_work: 0.3349 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10380 Z= 0.116 Angle : 0.480 5.044 13994 Z= 0.250 Chirality : 0.038 0.136 1516 Planarity : 0.004 0.060 1796 Dihedral : 4.415 53.825 1357 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.38 % Allowed : 17.71 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1219 helix: 1.65 (0.21), residues: 601 sheet: -0.64 (0.42), residues: 149 loop : 0.22 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 PHE 0.009 0.001 PHE A 930 TYR 0.012 0.001 TYR A 265 ARG 0.009 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 530) hydrogen bonds : angle 4.13930 ( 1491) covalent geometry : bond 0.00276 (10380) covalent geometry : angle 0.47977 (13994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10678.18 seconds wall clock time: 183 minutes 28.52 seconds (11008.52 seconds total)