Starting phenix.real_space_refine on Tue Jun 17 20:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tu6_41617/06_2025/8tu6_41617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tu6_41617/06_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_41617/06_2025/8tu6_41617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tu6_41617/06_2025/8tu6_41617.map" model { file = "/net/cci-nas-00/data/ceres_data/8tu6_41617/06_2025/8tu6_41617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tu6_41617/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.83, per 1000 atoms: 0.53 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: 5.47 Conformation dependent library (CDL) restraints added in 1.6 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: 1.98 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: 9.02 Time building geometry restraints manager: 6.76 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: 1.630 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: 0.320 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 48.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.360 ------------------------------------------------------------------------------- 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 : 1.575 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: 0.6673 time to fit residues: 137.7642 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 : 1.609 ------------------------------------------------------------------------------- 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 = 0.161597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126066 restraints weight = 35067.990| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.00 r_work: 0.3373 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0860 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= 0.135 Angle : 0.538 5.197 13994 Z= 0.286 Chirality : 0.039 0.142 1516 Planarity : 0.004 0.063 1796 Dihedral : 5.042 55.561 1361 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.23 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 0.04984 ( 530) hydrogen bonds : angle 4.87899 ( 1491) covalent geometry : bond 0.00303 (10380) covalent geometry : angle 0.53756 (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 : 1.708 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: 0.7946 (p90) cc_final: 0.7716 (p90) REVERT: A 108 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7926 (mtp-110) REVERT: A 184 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8069 (mmtt) REVERT: A 282 MET cc_start: 0.7550 (mtp) cc_final: 0.7266 (ttm) REVERT: A 288 MET cc_start: 0.7915 (ttm) cc_final: 0.7651 (ttt) REVERT: A 809 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: A 937 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8256 (p90) REVERT: A 975 ARG cc_start: 0.7446 (tmt170) cc_final: 0.7241 (tmt170) outliers start: 27 outliers final: 16 residues processed: 158 average time/residue: 0.6461 time to fit residues: 135.4737 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 : 1.658 ------------------------------------------------------------------------------- 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: 7.9990 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: 0.9980 chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.158765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122896 restraints weight = 35079.054| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.15 r_work: 0.3316 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10380 Z= 0.199 Angle : 0.556 6.769 13994 Z= 0.292 Chirality : 0.040 0.146 1516 Planarity : 0.005 0.066 1796 Dihedral : 5.083 56.309 1359 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 17.00 % 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: 0.62 (0.24), residues: 1219 helix: 1.05 (0.21), residues: 596 sheet: -0.52 (0.40), residues: 149 loop : 0.08 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 PHE 0.016 0.002 PHE A 930 TYR 0.009 0.001 TYR A 904 ARG 0.005 0.000 ARG A 808 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 530) hydrogen bonds : angle 4.68655 ( 1491) covalent geometry : bond 0.00476 (10380) covalent geometry : angle 0.55584 (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 166 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.7876 (p90) cc_final: 0.7676 (p90) REVERT: A 108 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7919 (mtp-110) REVERT: A 184 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8010 (mmtt) REVERT: A 219 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: A 448 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 561 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7935 (pt) REVERT: A 610 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8212 (mpp) REVERT: A 809 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7788 (pt0) REVERT: A 1012 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7543 (mt-10) outliers start: 31 outliers final: 18 residues processed: 155 average time/residue: 0.6228 time to fit residues: 129.4830 Evaluate side-chains 156 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE 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 303 THR 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 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: 2.9990 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.159464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124167 restraints weight = 35439.390| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.02 r_work: 0.3320 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10380 Z= 0.158 Angle : 0.519 5.688 13994 Z= 0.271 Chirality : 0.039 0.139 1516 Planarity : 0.004 0.057 1796 Dihedral : 4.880 57.120 1358 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.08 % Allowed : 16.21 % Favored : 80.70 % 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: 0.73 (0.25), residues: 1219 helix: 1.19 (0.21), residues: 598 sheet: -0.54 (0.41), residues: 149 loop : 0.08 (0.31), 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 0.012 0.001 PHE A 930 TYR 0.009 0.001 TYR A 265 ARG 0.006 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 530) hydrogen bonds : angle 4.49101 ( 1491) covalent geometry : bond 0.00377 (10380) covalent geometry : angle 0.51922 (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 178 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7271 (pp) REVERT: A 155 ASP cc_start: 0.7399 (m-30) cc_final: 0.6810 (t0) REVERT: A 184 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7973 (mmtt) REVERT: A 219 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: A 336 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8619 (mt) REVERT: A 448 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 561 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7908 (pt) REVERT: A 809 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: A 1012 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 380 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8911 (mt) REVERT: B 421 ASP cc_start: 0.7621 (t0) cc_final: 0.7058 (t0) outliers start: 35 outliers final: 21 residues processed: 170 average time/residue: 0.5675 time to fit residues: 133.1533 Evaluate side-chains 164 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 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 450 HIS Chi-restraints excluded: chain B residue 497 GLN 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: 2.9990 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: 1.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.159544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122336 restraints weight = 35532.856| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.01 r_work: 0.3313 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10380 Z= 0.161 Angle : 0.516 5.261 13994 Z= 0.270 Chirality : 0.039 0.142 1516 Planarity : 0.004 0.059 1796 Dihedral : 4.839 56.605 1358 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.17 % Allowed : 16.48 % Favored : 80.35 % 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: 1.24 (0.21), residues: 598 sheet: -0.65 (0.41), residues: 149 loop : 0.08 (0.31), residues: 472 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 0.013 0.001 PHE A 930 TYR 0.009 0.001 TYR A 265 ARG 0.006 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 530) hydrogen bonds : angle 4.43534 ( 1491) covalent geometry : bond 0.00387 (10380) covalent geometry : angle 0.51614 (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 174 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7336 (pp) REVERT: A 219 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7128 (mp10) REVERT: A 336 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8638 (mt) REVERT: A 448 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8610 (p) REVERT: A 561 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7889 (pt) REVERT: A 809 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7843 (pt0) REVERT: A 825 GLN cc_start: 0.7538 (mm110) cc_final: 0.7327 (mm-40) REVERT: B 380 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8925 (mt) REVERT: B 421 ASP cc_start: 0.7710 (t0) cc_final: 0.7120 (t0) REVERT: B 422 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8390 (p) outliers start: 36 outliers final: 22 residues processed: 163 average time/residue: 0.5566 time to fit residues: 126.5914 Evaluate side-chains 165 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 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 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 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 422 VAL Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 497 GLN 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: 2.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN A 940 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119489 restraints weight = 35719.349| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.02 r_work: 0.3293 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10380 Z= 0.262 Angle : 0.574 5.172 13994 Z= 0.302 Chirality : 0.042 0.152 1516 Planarity : 0.005 0.063 1796 Dihedral : 5.018 53.298 1358 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.79 % Allowed : 16.56 % Favored : 79.65 % 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: 0.33 (0.24), residues: 1219 helix: 0.95 (0.21), residues: 600 sheet: -0.75 (0.39), residues: 156 loop : -0.24 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 780 HIS 0.005 0.001 HIS A 701 PHE 0.017 0.002 PHE A 302 TYR 0.012 0.001 TYR A1038 ARG 0.007 0.001 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 530) hydrogen bonds : angle 4.60413 ( 1491) covalent geometry : bond 0.00643 (10380) covalent geometry : angle 0.57368 (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 177 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7366 (pp) REVERT: A 155 ASP cc_start: 0.7594 (m-30) cc_final: 0.7019 (t0) REVERT: A 219 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: A 448 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8662 (p) REVERT: A 561 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7943 (pt) REVERT: A 796 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7062 (p0) REVERT: A 973 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8283 (mmtp) REVERT: B 380 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8926 (mt) REVERT: B 421 ASP cc_start: 0.7721 (t0) cc_final: 0.7081 (t0) REVERT: B 422 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8347 (p) outliers start: 43 outliers final: 28 residues processed: 166 average time/residue: 0.5364 time to fit residues: 123.5771 Evaluate side-chains 167 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 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 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 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 416 TYR Chi-restraints excluded: chain B residue 422 VAL 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: 2.9990 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.123299 restraints weight = 35299.783| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.97 r_work: 0.3341 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2127 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= 0.118 Angle : 0.494 5.066 13994 Z= 0.259 Chirality : 0.038 0.139 1516 Planarity : 0.004 0.054 1796 Dihedral : 4.757 54.309 1358 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.82 % Allowed : 17.53 % Favored : 79.65 % 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: 0.74 (0.25), residues: 1219 helix: 1.30 (0.21), residues: 599 sheet: -0.68 (0.40), residues: 156 loop : -0.01 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 780 HIS 0.004 0.001 HIS A 940 PHE 0.009 0.001 PHE A 937 TYR 0.011 0.001 TYR A 265 ARG 0.008 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 530) hydrogen bonds : angle 4.34102 ( 1491) covalent geometry : bond 0.00275 (10380) covalent geometry : angle 0.49365 (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 166 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.694 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: 0.7612 (OUTLIER) cc_final: 0.7405 (pp) REVERT: A 155 ASP cc_start: 0.7478 (m-30) cc_final: 0.6965 (t0) REVERT: A 219 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: A 561 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7885 (pt) REVERT: A 709 MET cc_start: 0.8769 (mmp) cc_final: 0.8535 (mmp) REVERT: A 796 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7051 (p0) REVERT: A 809 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: A 825 GLN cc_start: 0.7495 (mm110) cc_final: 0.7233 (mm-40) REVERT: A 973 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8263 (mmtp) REVERT: B 380 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8938 (mt) REVERT: B 421 ASP cc_start: 0.7734 (t0) cc_final: 0.7150 (t0) REVERT: B 422 VAL cc_start: 0.8612 (p) cc_final: 0.8406 (p) outliers start: 32 outliers final: 23 residues processed: 156 average time/residue: 0.5414 time to fit residues: 117.3600 Evaluate side-chains 160 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 331 ASN 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 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 380 LEU Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 497 GLN 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: 4.9990 chunk 54 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 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 = 0.159854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125020 restraints weight = 35186.084| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.00 r_work: 0.3343 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10380 Z= 0.113 Angle : 0.485 5.047 13994 Z= 0.254 Chirality : 0.038 0.137 1516 Planarity : 0.004 0.056 1796 Dihedral : 4.683 54.582 1358 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.82 % Allowed : 17.71 % Favored : 79.47 % 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: 0.87 (0.25), residues: 1219 helix: 1.43 (0.21), residues: 599 sheet: -0.67 (0.40), residues: 156 loop : 0.06 (0.31), residues: 464 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 937 TYR 0.011 0.001 TYR A 265 ARG 0.008 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 530) hydrogen bonds : angle 4.28186 ( 1491) covalent geometry : bond 0.00266 (10380) covalent geometry : angle 0.48472 (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 169 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7379 (pp) REVERT: A 155 ASP cc_start: 0.7475 (m-30) cc_final: 0.6952 (t0) REVERT: A 219 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: A 561 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7887 (pt) REVERT: A 796 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7019 (p0) REVERT: A 809 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7821 (pt0) REVERT: A 825 GLN cc_start: 0.7457 (mm110) cc_final: 0.7225 (mm-40) REVERT: A 973 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8311 (mmtp) REVERT: A 1012 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 380 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8902 (mt) REVERT: B 421 ASP cc_start: 0.7758 (t0) cc_final: 0.7158 (t0) REVERT: B 422 VAL cc_start: 0.8616 (p) cc_final: 0.8409 (p) outliers start: 32 outliers final: 22 residues processed: 159 average time/residue: 0.5458 time to fit residues: 121.2962 Evaluate side-chains 159 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 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 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 380 LEU Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 497 GLN 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: 0.4980 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.160098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123592 restraints weight = 35240.459| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.00 r_work: 0.3337 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10380 Z= 0.103 Angle : 0.471 5.030 13994 Z= 0.245 Chirality : 0.037 0.138 1516 Planarity : 0.004 0.060 1796 Dihedral : 4.515 55.666 1358 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.94 % Allowed : 18.15 % 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: 1.09 (0.25), residues: 1219 helix: 1.60 (0.21), residues: 599 sheet: -0.68 (0.42), residues: 149 loop : 0.20 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 PHE 0.009 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 0.03450 ( 530) hydrogen bonds : angle 4.15786 ( 1491) covalent geometry : bond 0.00243 (10380) covalent geometry : angle 0.47069 (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 157 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7341 (pp) REVERT: A 155 ASP cc_start: 0.7488 (m-30) cc_final: 0.6946 (t0) REVERT: A 675 MET cc_start: 0.8195 (tpp) cc_final: 0.7937 (tpp) REVERT: A 796 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.6968 (p0) REVERT: A 809 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: A 820 MET cc_start: 0.8197 (ptp) cc_final: 0.7933 (ptp) REVERT: A 825 GLN cc_start: 0.7462 (mm110) cc_final: 0.7226 (mm-40) REVERT: A 973 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8341 (mmtp) REVERT: A 1012 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7568 (mt-10) REVERT: B 421 ASP cc_start: 0.7755 (t0) cc_final: 0.7155 (t0) outliers start: 22 outliers final: 17 residues processed: 149 average time/residue: 0.5408 time to fit residues: 112.4561 Evaluate side-chains 148 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 650 VAL Chi-restraints excluded: chain A residue 779 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 450 HIS Chi-restraints excluded: chain B residue 497 GLN 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: 0.7980 chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.157697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125605 restraints weight = 35088.151| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.80 r_work: 0.3354 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2417 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= 0.120 Angle : 0.483 5.034 13994 Z= 0.252 Chirality : 0.038 0.137 1516 Planarity : 0.004 0.060 1796 Dihedral : 4.446 55.069 1357 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.94 % Allowed : 18.06 % 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: 1.09 (0.25), residues: 1219 helix: 1.61 (0.21), residues: 601 sheet: -0.69 (0.42), residues: 149 loop : 0.19 (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 0.010 0.001 PHE A 930 TYR 0.010 0.001 TYR A 265 ARG 0.008 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 530) hydrogen bonds : angle 4.15582 ( 1491) covalent geometry : bond 0.00286 (10380) covalent geometry : angle 0.48340 (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 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7355 (pp) REVERT: A 675 MET cc_start: 0.8198 (tpp) cc_final: 0.7932 (tpp) REVERT: A 796 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.6952 (p0) REVERT: A 820 MET cc_start: 0.8126 (ptp) cc_final: 0.7854 (ptp) REVERT: A 888 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7020 (tm-30) REVERT: A 973 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8388 (mmtp) REVERT: A 1012 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 421 ASP cc_start: 0.7844 (t0) cc_final: 0.7191 (t0) outliers start: 22 outliers final: 18 residues processed: 141 average time/residue: 0.5633 time to fit residues: 111.0092 Evaluate side-chains 146 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 296 GLN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 796 ASN 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 450 HIS Chi-restraints excluded: chain B residue 497 GLN 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: 0.6980 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 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: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.157790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125674 restraints weight = 35246.322| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.81 r_work: 0.3355 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 10380 Z= 0.170 Angle : 0.816 59.174 13994 Z= 0.489 Chirality : 0.039 0.338 1516 Planarity : 0.004 0.059 1796 Dihedral : 4.456 55.070 1357 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.94 % Allowed : 17.97 % Favored : 80.09 % Cbeta Deviations : 0.08 % 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: 1.10 (0.25), residues: 1219 helix: 1.61 (0.21), residues: 601 sheet: -0.69 (0.42), residues: 149 loop : 0.19 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 780 HIS 0.002 0.001 HIS A 665 PHE 0.010 0.001 PHE A 930 TYR 0.010 0.001 TYR A 265 ARG 0.005 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 530) hydrogen bonds : angle 4.15532 ( 1491) covalent geometry : bond 0.00365 (10380) covalent geometry : angle 0.81624 (13994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11059.79 seconds wall clock time: 187 minutes 45.95 seconds (11265.95 seconds total)