Starting phenix.real_space_refine on Sun Aug 24 13:49:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tu6_41617/08_2025/8tu6_41617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tu6_41617/08_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_41617/08_2025/8tu6_41617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tu6_41617/08_2025/8tu6_41617.map" model { file = "/net/cci-nas-00/data/ceres_data/8tu6_41617/08_2025/8tu6_41617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tu6_41617/08_2025/8tu6_41617.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.90, per 1000 atoms: 0.19 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: 1.85 Conformation dependent library (CDL) restraints added in 534.2 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 0.62 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: 5.17 Time building geometry restraints manager: 2.61 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (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 ARG 0.013 0.001 ARG A 741 TYR 0.012 0.001 TYR A 904 PHE 0.011 0.001 PHE A 667 TRP 0.011 0.001 TRP A 780 HIS 0.008 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00393 (10380) covalent geometry : angle 0.59143 (13994) hydrogen bonds : bond 0.17149 ( 530) hydrogen bonds : angle 6.43182 ( 1491) *********************** 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 : 0.592 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: 0.3473 time to fit residues: 71.0376 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 : 0.585 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 797 ASN A 825 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.160602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124482 restraints weight = 35214.696| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.13 r_work: 0.3354 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10380 Z= 0.147 Angle : 0.546 5.144 13994 Z= 0.289 Chirality : 0.039 0.142 1516 Planarity : 0.005 0.064 1796 Dihedral : 5.088 55.633 1361 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.47 % Allowed : 17.36 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.24), residues: 1219 helix: 1.08 (0.21), residues: 595 sheet: -0.29 (0.38), residues: 158 loop : 0.21 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 975 TYR 0.009 0.001 TYR A 904 PHE 0.013 0.001 PHE A 930 TRP 0.012 0.001 TRP A 780 HIS 0.005 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00341 (10380) covalent geometry : angle 0.54610 (13994) hydrogen bonds : bond 0.04676 ( 530) hydrogen bonds : angle 4.83329 ( 1491) *********************** 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: 28 poor density : 139 time to evaluate : 0.459 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 59 HIS cc_start: 0.7875 (p90) cc_final: 0.7662 (p90) REVERT: A 108 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7929 (mtp-110) REVERT: A 184 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8071 (mmtt) REVERT: A 282 MET cc_start: 0.7584 (mtp) cc_final: 0.7312 (ttm) REVERT: A 288 MET cc_start: 0.7928 (ttm) cc_final: 0.7662 (ttt) REVERT: A 937 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8329 (p90) outliers start: 28 outliers final: 17 residues processed: 158 average time/residue: 0.2584 time to fit residues: 54.5570 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 : 0.431 ------------------------------------------------------------------------------- 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 109 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.161954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126038 restraints weight = 35023.440| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.13 r_work: 0.3369 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10380 Z= 0.113 Angle : 0.497 6.955 13994 Z= 0.258 Chirality : 0.038 0.137 1516 Planarity : 0.004 0.051 1796 Dihedral : 4.814 58.998 1359 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.38 % Allowed : 16.83 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.25), residues: 1219 helix: 1.36 (0.21), residues: 595 sheet: -0.48 (0.40), residues: 149 loop : 0.32 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 740 TYR 0.009 0.001 TYR A 904 PHE 0.010 0.001 PHE A 960 TRP 0.011 0.001 TRP A 780 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00262 (10380) covalent geometry : angle 0.49684 (13994) hydrogen bonds : bond 0.04050 ( 530) hydrogen bonds : angle 4.44632 ( 1491) *********************** 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 167 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7972 (mmtt) REVERT: A 219 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: A 288 MET cc_start: 0.7912 (ttm) cc_final: 0.7674 (ttt) REVERT: A 390 ASP cc_start: 0.8107 (m-30) cc_final: 0.7873 (t0) REVERT: A 489 MET cc_start: 0.6832 (mmm) cc_final: 0.6516 (mmm) REVERT: A 561 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7903 (pt) REVERT: A 809 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: A 937 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8279 (p90) REVERT: B 421 ASP cc_start: 0.7544 (t0) cc_final: 0.7017 (t0) outliers start: 27 outliers final: 15 residues processed: 156 average time/residue: 0.2999 time to fit residues: 63.1142 Evaluate side-chains 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 434 ASP 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 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 365 HIS Chi-restraints excluded: chain B residue 460 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 35 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.160914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123565 restraints weight = 35299.177| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.03 r_work: 0.3335 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1683 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= 0.139 Angle : 0.502 5.455 13994 Z= 0.261 Chirality : 0.038 0.137 1516 Planarity : 0.004 0.056 1796 Dihedral : 4.710 58.953 1358 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.73 % Allowed : 16.74 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.25), residues: 1219 helix: 1.43 (0.21), residues: 597 sheet: -0.46 (0.41), residues: 149 loop : 0.27 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 740 TYR 0.009 0.001 TYR A 904 PHE 0.012 0.001 PHE A 930 TRP 0.012 0.001 TRP A 780 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00330 (10380) covalent geometry : angle 0.50183 (13994) hydrogen bonds : bond 0.03878 ( 530) hydrogen bonds : angle 4.34982 ( 1491) *********************** 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 166 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.599 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: 0.7499 (OUTLIER) cc_final: 0.7264 (pp) REVERT: A 184 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7960 (mmtt) REVERT: A 219 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: A 288 MET cc_start: 0.7934 (ttm) cc_final: 0.7693 (ttt) REVERT: A 448 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 675 MET cc_start: 0.8296 (tpp) cc_final: 0.7972 (tpp) REVERT: A 809 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: B 421 ASP cc_start: 0.7608 (t0) cc_final: 0.7009 (t0) outliers start: 31 outliers final: 18 residues processed: 156 average time/residue: 0.2910 time to fit residues: 61.7905 Evaluate side-chains 150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 448 VAL 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 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 422 VAL Chi-restraints excluded: chain B residue 450 HIS Chi-restraints excluded: chain B residue 538 ILE 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 79 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.159638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124395 restraints weight = 35100.070| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.02 r_work: 0.3336 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1861 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= 0.169 Angle : 0.513 5.350 13994 Z= 0.269 Chirality : 0.039 0.144 1516 Planarity : 0.004 0.057 1796 Dihedral : 4.759 57.605 1358 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.00 % Allowed : 16.12 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.25), residues: 1219 helix: 1.32 (0.21), residues: 598 sheet: -0.52 (0.41), residues: 149 loop : 0.20 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 740 TYR 0.009 0.001 TYR A1038 PHE 0.013 0.002 PHE A 930 TRP 0.012 0.001 TRP A 780 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00406 (10380) covalent geometry : angle 0.51343 (13994) hydrogen bonds : bond 0.03995 ( 530) hydrogen bonds : angle 4.37457 ( 1491) *********************** 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 166 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.361 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: 0.7565 (OUTLIER) cc_final: 0.7334 (pp) REVERT: A 155 ASP cc_start: 0.7452 (m-30) cc_final: 0.6842 (t0) REVERT: A 219 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: A 288 MET cc_start: 0.7927 (ttm) cc_final: 0.7684 (ttt) REVERT: A 336 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 448 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 561 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7885 (pt) REVERT: A 809 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: A 825 GLN cc_start: 0.7561 (mm110) cc_final: 0.7350 (mm-40) REVERT: A 973 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8273 (mmtp) REVERT: B 380 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8905 (mt) REVERT: B 421 ASP cc_start: 0.7712 (t0) cc_final: 0.7088 (t0) outliers start: 34 outliers final: 22 residues processed: 154 average time/residue: 0.2249 time to fit residues: 48.2814 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 : 0.434 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124816 restraints weight = 35184.764| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.02 r_work: 0.3329 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10380 Z= 0.151 Angle : 0.498 5.598 13994 Z= 0.260 Chirality : 0.038 0.142 1516 Planarity : 0.004 0.053 1796 Dihedral : 4.698 56.974 1358 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.00 % Allowed : 16.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.25), residues: 1219 helix: 1.39 (0.21), residues: 598 sheet: -0.57 (0.41), residues: 149 loop : 0.14 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 740 TYR 0.009 0.001 TYR A 904 PHE 0.012 0.001 PHE A 930 TRP 0.012 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00363 (10380) covalent geometry : angle 0.49753 (13994) hydrogen bonds : bond 0.03847 ( 530) hydrogen bonds : angle 4.32506 ( 1491) *********************** 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 169 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7328 (pp) REVERT: A 155 ASP cc_start: 0.7449 (m-30) cc_final: 0.6929 (t0) REVERT: A 219 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: A 288 MET cc_start: 0.7912 (ttm) cc_final: 0.7656 (ttt) REVERT: A 336 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8625 (mt) REVERT: A 448 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8589 (p) REVERT: A 561 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7888 (pt) REVERT: A 796 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7003 (p0) REVERT: A 809 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: A 973 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8282 (mmtp) REVERT: A 1012 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7502 (mt-10) REVERT: B 380 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8900 (mt) REVERT: B 421 ASP cc_start: 0.7732 (t0) cc_final: 0.7109 (t0) REVERT: B 422 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8400 (p) outliers start: 34 outliers final: 20 residues processed: 158 average time/residue: 0.2680 time to fit residues: 58.8790 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 : 0.645 ------------------------------------------------------------------------------- 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 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 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 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 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 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 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.160518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123259 restraints weight = 35354.524| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.02 r_work: 0.3343 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2089 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= 0.129 Angle : 0.483 5.919 13994 Z= 0.253 Chirality : 0.038 0.138 1516 Planarity : 0.004 0.057 1796 Dihedral : 4.615 56.530 1358 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.56 % Allowed : 16.92 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.25), residues: 1219 helix: 1.49 (0.21), residues: 598 sheet: -0.59 (0.41), residues: 149 loop : 0.20 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 740 TYR 0.009 0.001 TYR A 904 PHE 0.010 0.001 PHE A 930 TRP 0.010 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00309 (10380) covalent geometry : angle 0.48295 (13994) hydrogen bonds : bond 0.03693 ( 530) hydrogen bonds : angle 4.24976 ( 1491) *********************** 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 167 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7251 (pp) REVERT: A 155 ASP cc_start: 0.7467 (m-30) cc_final: 0.6912 (t0) REVERT: A 219 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: A 288 MET cc_start: 0.7921 (ttm) cc_final: 0.7639 (ttt) REVERT: A 336 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8614 (mt) REVERT: A 561 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7867 (pt) REVERT: A 809 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: A 825 GLN cc_start: 0.7500 (mm110) cc_final: 0.7262 (mm-40) REVERT: A 973 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8332 (mmtp) REVERT: A 1012 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 380 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8857 (mt) REVERT: B 421 ASP cc_start: 0.7720 (t0) cc_final: 0.7087 (t0) REVERT: B 422 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8398 (p) outliers start: 29 outliers final: 18 residues processed: 159 average time/residue: 0.2622 time to fit residues: 57.0188 Evaluate side-chains 154 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 650 VAL 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 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 563 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.157226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120224 restraints weight = 35699.635| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.99 r_work: 0.3290 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10380 Z= 0.237 Angle : 0.554 5.909 13994 Z= 0.292 Chirality : 0.041 0.150 1516 Planarity : 0.005 0.061 1796 Dihedral : 4.765 53.122 1357 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.35 % Allowed : 16.56 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.25), residues: 1219 helix: 1.18 (0.21), residues: 599 sheet: -0.72 (0.41), residues: 149 loop : -0.03 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 740 TYR 0.011 0.001 TYR A1038 PHE 0.017 0.002 PHE A 302 TRP 0.013 0.002 TRP A 780 HIS 0.004 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00577 (10380) covalent geometry : angle 0.55384 (13994) hydrogen bonds : bond 0.04242 ( 530) hydrogen bonds : angle 4.45862 ( 1491) *********************** 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: 38 poor density : 131 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7394 (pp) REVERT: A 219 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: A 288 MET cc_start: 0.7987 (ttm) cc_final: 0.7733 (ttt) REVERT: A 336 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8604 (mt) REVERT: A 448 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 561 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7935 (pt) REVERT: A 796 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7148 (p0) REVERT: A 809 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: A 820 MET cc_start: 0.8438 (ptp) cc_final: 0.8058 (ptp) REVERT: A 886 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8279 (mtmt) REVERT: A 973 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8344 (mmtp) REVERT: B 380 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8931 (mt) REVERT: B 421 ASP cc_start: 0.7773 (t0) cc_final: 0.7124 (t0) REVERT: B 422 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8447 (p) outliers start: 38 outliers final: 22 residues processed: 161 average time/residue: 0.2690 time to fit residues: 60.3929 Evaluate side-chains 163 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.159422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122218 restraints weight = 35232.803| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.04 r_work: 0.3328 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10380 Z= 0.137 Angle : 0.499 6.374 13994 Z= 0.261 Chirality : 0.038 0.141 1516 Planarity : 0.005 0.060 1796 Dihedral : 4.612 52.752 1357 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.56 % Allowed : 17.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1219 helix: 1.34 (0.21), residues: 601 sheet: -0.69 (0.41), residues: 149 loop : 0.07 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 740 TYR 0.010 0.001 TYR A 904 PHE 0.010 0.001 PHE A 930 TRP 0.010 0.001 TRP A 780 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00327 (10380) covalent geometry : angle 0.49921 (13994) hydrogen bonds : bond 0.03769 ( 530) hydrogen bonds : angle 4.26850 ( 1491) *********************** 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 164 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7331 (pp) REVERT: A 155 ASP cc_start: 0.7524 (m-30) cc_final: 0.6934 (t0) REVERT: A 219 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7097 (mp10) REVERT: A 288 MET cc_start: 0.7932 (ttm) cc_final: 0.7645 (ttt) REVERT: A 336 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 561 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7903 (pt) REVERT: A 796 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.6993 (p0) REVERT: A 809 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: A 820 MET cc_start: 0.8313 (ptp) cc_final: 0.8048 (ptp) REVERT: A 886 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8252 (mtmt) REVERT: A 973 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8347 (mmtp) REVERT: A 1012 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 380 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8896 (mt) REVERT: B 421 ASP cc_start: 0.7799 (t0) cc_final: 0.7153 (t0) REVERT: B 422 VAL cc_start: 0.8637 (p) cc_final: 0.8425 (p) outliers start: 29 outliers final: 21 residues processed: 157 average time/residue: 0.2392 time to fit residues: 52.1978 Evaluate side-chains 162 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 A residue 1024 LYS 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 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 0 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.159799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122931 restraints weight = 35350.618| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.00 r_work: 0.3329 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10380 Z= 0.138 Angle : 0.498 6.388 13994 Z= 0.260 Chirality : 0.038 0.139 1516 Planarity : 0.005 0.061 1796 Dihedral : 4.526 52.054 1357 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 17.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.25), residues: 1219 helix: 1.42 (0.21), residues: 601 sheet: -0.67 (0.42), residues: 149 loop : 0.12 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 740 TYR 0.009 0.001 TYR A 904 PHE 0.011 0.001 PHE A 930 TRP 0.008 0.001 TRP A 780 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00332 (10380) covalent geometry : angle 0.49752 (13994) hydrogen bonds : bond 0.03687 ( 530) hydrogen bonds : angle 4.20499 ( 1491) ********************** 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 162 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7410 (pp) REVERT: A 155 ASP cc_start: 0.7497 (m-30) cc_final: 0.6970 (t0) REVERT: A 219 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: A 288 MET cc_start: 0.7947 (ttm) cc_final: 0.7678 (ttt) REVERT: A 336 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8614 (mt) REVERT: A 561 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7888 (pt) REVERT: A 796 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7022 (p0) REVERT: A 809 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: A 820 MET cc_start: 0.8289 (ptp) cc_final: 0.7984 (ptp) REVERT: A 886 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8261 (mtmt) REVERT: A 888 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 973 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8395 (mmtp) REVERT: A 975 ARG cc_start: 0.7478 (tmt170) cc_final: 0.7211 (ttp80) REVERT: A 1012 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 380 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8908 (mt) REVERT: B 421 ASP cc_start: 0.7748 (t0) cc_final: 0.7122 (t0) outliers start: 27 outliers final: 19 residues processed: 155 average time/residue: 0.2451 time to fit residues: 53.0066 Evaluate side-chains 157 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 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 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 19 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 49 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126001 restraints weight = 35194.444| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.95 r_work: 0.3367 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10380 Z= 0.101 Angle : 0.478 6.400 13994 Z= 0.248 Chirality : 0.037 0.138 1516 Planarity : 0.004 0.060 1796 Dihedral : 4.375 52.323 1357 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.85 % Allowed : 17.62 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.25), residues: 1219 helix: 1.61 (0.21), residues: 602 sheet: -0.60 (0.42), residues: 149 loop : 0.27 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 740 TYR 0.010 0.001 TYR A 904 PHE 0.008 0.001 PHE A 930 TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00239 (10380) covalent geometry : angle 0.47832 (13994) hydrogen bonds : bond 0.03403 ( 530) hydrogen bonds : angle 4.07594 ( 1491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5487.14 seconds wall clock time: 93 minutes 46.63 seconds (5626.63 seconds total)