Starting phenix.real_space_refine on Sat Dec 28 21:48:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rph_24614/12_2024/7rph_24614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rph_24614/12_2024/7rph_24614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rph_24614/12_2024/7rph_24614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rph_24614/12_2024/7rph_24614.map" model { file = "/net/cci-nas-00/data/ceres_data/7rph_24614/12_2024/7rph_24614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rph_24614/12_2024/7rph_24614.cif" } resolution = 2.5 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= 0.006 sd= 0.579 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 65 5.16 5 Na 3 4.78 5 C 5742 2.51 5 N 1185 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8573 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 7358 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 926, 7358 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885} Chain breaks: 3 bond proxies already assigned to first conformer: 7547 Chain: "A" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1207 Unusual residues: {' NA': 3, 'AV0': 2, 'NAG': 5, 'Y01': 26} Classifications: {'undetermined': 36, 'water': 86} Link IDs: {None: 121} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 557 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 557 " occ=0.50 Time building chain proxies: 9.54, per 1000 atoms: 1.11 Number of scatterers: 8573 At special positions: 0 Unit cell: (88.51, 88.51, 127.755, 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 65 16.00 Na 3 11.00 O 1578 8.00 N 1185 7.00 C 5742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.04 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.05 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.05 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 Links applied NAG-ASN " NAG A1632 " - " ASN A 915 " " NAG A1633 " - " ASN A 475 " " NAG A1634 " - " ASN A 834 " " NAG A1635 " - " ASN A 362 " " NAG A1636 " - " ASN A 390 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.8 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 3 sheets defined 67.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.550A pdb=" N VAL A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.606A pdb=" N ARG A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.547A pdb=" N CYS A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 390 removed outlier: 3.518A pdb=" N VAL A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 388 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.973A pdb=" N THR A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.001A pdb=" N ASP A 442 " --> pdb=" O PRO A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.567A pdb=" N TYR A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 523 through 548 removed outlier: 3.813A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 570 through 587 Processing helix chain 'A' and resid 591 through 621 removed outlier: 5.641A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 626 through 648 Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 682 through 706 Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.581A pdb=" N CYS A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 736 removed outlier: 3.527A pdb=" N ILE A 721 " --> pdb=" O TYR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.646A pdb=" N ASP A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 779 removed outlier: 4.013A pdb=" N HIS A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 834 removed outlier: 3.547A pdb=" N ASN A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 859 removed outlier: 3.763A pdb=" N THR A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Proline residue: A 870 - end of helix Processing helix chain 'A' and resid 880 through 899 removed outlier: 4.099A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 954 removed outlier: 3.514A pdb=" N GLN A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1002 Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1033 through 1061 removed outlier: 3.719A pdb=" N VAL A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1094 removed outlier: 5.233A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1123 Processing helix chain 'A' and resid 1123 through 1133 Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458 removed outlier: 3.952A pdb=" N SER A 300 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG A 301 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE A 486 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 303 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 343 removed outlier: 4.828A pdb=" N THR A 343 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 910 through 912 removed outlier: 7.955A pdb=" N LEU A 923 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TRP A 789 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE A 925 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 787 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER A 927 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 785 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE A 929 " --> pdb=" O MET A 783 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1287 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: 3.18 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1239 1.29 - 1.42: 2196 1.42 - 1.56: 4867 1.56 - 1.69: 367 1.69 - 1.83: 98 Bond restraints: 8767 Sorted by residual: bond pdb=" C LEU A1086 " pdb=" O LEU A1086 " ideal model delta sigma weight residual 1.237 1.156 0.081 1.17e-02 7.31e+03 4.75e+01 bond pdb=" C THR A 613 " pdb=" O THR A 613 " ideal model delta sigma weight residual 1.236 1.150 0.086 1.26e-02 6.30e+03 4.71e+01 bond pdb=" C ALA A 615 " pdb=" O ALA A 615 " ideal model delta sigma weight residual 1.237 1.159 0.078 1.16e-02 7.43e+03 4.53e+01 bond pdb=" C PHE A 608 " pdb=" O PHE A 608 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.16e-02 7.43e+03 4.18e+01 bond pdb=" C ALA A 573 " pdb=" O ALA A 573 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.19e-02 7.06e+03 4.08e+01 ... (remaining 8762 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 8682 1.94 - 3.87: 2828 3.87 - 5.81: 493 5.81 - 7.75: 53 7.75 - 9.69: 10 Bond angle restraints: 12066 Sorted by residual: angle pdb=" N PHE A 612 " pdb=" CA PHE A 612 " pdb=" C PHE A 612 " ideal model delta sigma weight residual 111.71 121.40 -9.69 1.15e+00 7.56e-01 7.10e+01 angle pdb=" N LEU A1086 " pdb=" CA LEU A1086 " pdb=" C LEU A1086 " ideal model delta sigma weight residual 111.28 119.12 -7.84 1.09e+00 8.42e-01 5.17e+01 angle pdb=" CA PHE A 759 " pdb=" CB PHE A 759 " pdb=" CG PHE A 759 " ideal model delta sigma weight residual 113.80 120.09 -6.29 1.00e+00 1.00e+00 3.96e+01 angle pdb=" N ASP A1049 " pdb=" CA ASP A1049 " pdb=" C ASP A1049 " ideal model delta sigma weight residual 111.07 117.58 -6.51 1.07e+00 8.73e-01 3.70e+01 angle pdb=" N ASP A 571 " pdb=" CA ASP A 571 " pdb=" C ASP A 571 " ideal model delta sigma weight residual 111.33 118.66 -7.33 1.21e+00 6.83e-01 3.67e+01 ... (remaining 12061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 6352 27.95 - 55.91: 258 55.91 - 83.86: 25 83.86 - 111.82: 15 111.82 - 139.77: 9 Dihedral angle restraints: 6659 sinusoidal: 3931 harmonic: 2728 Sorted by residual: dihedral pdb=" CB CYS A 863 " pdb=" SG CYS A 863 " pdb=" SG CYS A 872 " pdb=" CB CYS A 872 " ideal model delta sinusoidal sigma weight residual -86.00 -163.15 77.15 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CA VAL A1048 " pdb=" C VAL A1048 " pdb=" N ASP A1049 " pdb=" CA ASP A1049 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 134.34 -41.34 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 6656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 971 0.109 - 0.219: 384 0.219 - 0.328: 70 0.328 - 0.437: 14 0.437 - 0.546: 2 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA LEU A1086 " pdb=" N LEU A1086 " pdb=" C LEU A1086 " pdb=" CB LEU A1086 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CA PHE A 612 " pdb=" N PHE A 612 " pdb=" C PHE A 612 " pdb=" CB PHE A 612 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CA GLN A 334 " pdb=" N GLN A 334 " pdb=" C GLN A 334 " pdb=" CB GLN A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 1438 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 475 " 0.125 2.00e-02 2.50e+03 1.32e-01 2.17e+02 pdb=" CG ASN A 475 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 475 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 475 " -0.202 2.00e-02 2.50e+03 pdb=" C1 NAG A1633 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.134 2.00e-02 2.50e+03 6.63e-02 1.10e+02 pdb=" CG TRP A 313 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " -0.037 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.079 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.045 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 351 " -0.106 2.00e-02 2.50e+03 5.66e-02 8.00e+01 pdb=" CG TRP A 351 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 351 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TRP A 351 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP A 351 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 351 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP A 351 " 0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 351 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 351 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 351 " -0.052 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 19 2.54 - 3.13: 6250 3.13 - 3.72: 12578 3.72 - 4.31: 19701 4.31 - 4.90: 31303 Nonbonded interactions: 69851 Sorted by model distance: nonbonded pdb=" OD1 ASP A 571 " pdb="NA NA A1602 " model vdw 1.952 2.470 nonbonded pdb=" OD1 ASP A1049 " pdb="NA NA A1601 " model vdw 2.174 2.470 nonbonded pdb=" O GLY A 567 " pdb="NA NA A1602 " model vdw 2.186 2.470 nonbonded pdb=" OG1 THR A 613 " pdb="NA NA A1601 " model vdw 2.201 2.470 nonbonded pdb=" OD2 ASP A 572 " pdb="NA NA A1603 " model vdw 2.251 2.470 ... (remaining 69846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 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: 8.750 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.030 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.017 0.128 8767 Z= 1.014 Angle : 1.889 9.687 12066 Z= 1.230 Chirality : 0.115 0.546 1441 Planarity : 0.014 0.105 1340 Dihedral : 15.182 139.770 4869 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.61 % Allowed : 3.56 % Favored : 95.82 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 2.50 % 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: -0.70 (0.25), residues: 921 helix: -0.48 (0.19), residues: 563 sheet: -0.16 (0.97), residues: 29 loop : -0.11 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.021 TRP A 313 HIS 0.019 0.004 HIS A 777 PHE 0.065 0.012 PHE A 929 TYR 0.110 0.020 TYR A 762 ARG 0.008 0.001 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6381 (mtm) cc_final: 0.5288 (mmp) REVERT: A 198 LEU cc_start: 0.7679 (mt) cc_final: 0.7339 (mt) REVERT: A 256 TYR cc_start: 0.6588 (t80) cc_final: 0.6197 (t80) REVERT: A 364 SER cc_start: 0.7742 (m) cc_final: 0.7072 (t) REVERT: A 449 LYS cc_start: 0.7677 (tttt) cc_final: 0.7436 (tttm) REVERT: A 478 ASP cc_start: 0.7320 (t0) cc_final: 0.7104 (t70) REVERT: A 524 MET cc_start: 0.6868 (tpt) cc_final: 0.6467 (tpt) REVERT: A 754 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6093 (ptt90) REVERT: A 774 ARG cc_start: 0.6698 (mtp85) cc_final: 0.6093 (mtt-85) REVERT: A 840 GLN cc_start: 0.7642 (mt0) cc_final: 0.6944 (mp10) REVERT: A 846 PHE cc_start: 0.7302 (m-80) cc_final: 0.6841 (m-10) REVERT: A 852 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 858 MET cc_start: 0.8132 (mmm) cc_final: 0.7691 (mmt) REVERT: A 936 GLU cc_start: 0.7275 (tp30) cc_final: 0.6898 (mp0) REVERT: A 968 ASN cc_start: 0.7907 (m-40) cc_final: 0.7029 (t0) REVERT: A 1095 MET cc_start: 0.8652 (mmm) cc_final: 0.8357 (mmp) outliers start: 4 outliers final: 0 residues processed: 148 average time/residue: 1.2763 time to fit residues: 201.6804 Evaluate side-chains 111 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.0370 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 367 GLN A 376 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 856 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8767 Z= 0.170 Angle : 0.694 9.540 12066 Z= 0.326 Chirality : 0.046 0.340 1441 Planarity : 0.004 0.040 1340 Dihedral : 12.204 167.812 3202 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.60 % Allowed : 7.62 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.53 (0.28), residues: 921 helix: 1.40 (0.21), residues: 579 sheet: 0.21 (0.94), residues: 29 loop : 0.57 (0.39), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 313 HIS 0.005 0.001 HIS A 428 PHE 0.013 0.001 PHE A 454 TYR 0.017 0.002 TYR A 762 ARG 0.002 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6166 (mtm) cc_final: 0.5075 (mmp) REVERT: A 198 LEU cc_start: 0.7548 (mt) cc_final: 0.7313 (mt) REVERT: A 259 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6054 (tm-30) REVERT: A 321 MET cc_start: 0.7546 (mtm) cc_final: 0.7307 (mtm) REVERT: A 478 ASP cc_start: 0.7264 (t0) cc_final: 0.6974 (t70) REVERT: A 515 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6497 (tp) REVERT: A 754 ARG cc_start: 0.7380 (ptp-110) cc_final: 0.5933 (ptt90) REVERT: A 768 LYS cc_start: 0.7074 (mtmt) cc_final: 0.6353 (mttt) REVERT: A 774 ARG cc_start: 0.6731 (mtp85) cc_final: 0.6109 (mtt-85) REVERT: A 840 GLN cc_start: 0.7341 (mt0) cc_final: 0.6649 (mp10) REVERT: A 846 PHE cc_start: 0.7214 (m-80) cc_final: 0.6987 (m-80) REVERT: A 882 GLU cc_start: 0.5887 (pm20) cc_final: 0.5492 (mp0) REVERT: A 936 GLU cc_start: 0.6987 (tp30) cc_final: 0.6700 (mp0) REVERT: A 937 LYS cc_start: 0.7261 (ttpt) cc_final: 0.6874 (tptp) REVERT: A 968 ASN cc_start: 0.7885 (m-40) cc_final: 0.7021 (t0) REVERT: A 1011 ILE cc_start: 0.7022 (tp) cc_final: 0.6517 (pt) REVERT: A 1077 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7583 (mmm) outliers start: 12 outliers final: 5 residues processed: 137 average time/residue: 1.1324 time to fit residues: 166.4612 Evaluate side-chains 108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1077 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.0570 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8767 Z= 0.156 Angle : 0.616 7.846 12066 Z= 0.290 Chirality : 0.042 0.236 1441 Planarity : 0.004 0.038 1340 Dihedral : 11.172 175.407 3198 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.46 % Allowed : 9.21 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.96 (0.28), residues: 921 helix: 1.81 (0.21), residues: 579 sheet: 0.28 (0.91), residues: 31 loop : 0.59 (0.39), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 650 HIS 0.003 0.001 HIS A 428 PHE 0.012 0.001 PHE A 608 TYR 0.015 0.001 TYR A 467 ARG 0.002 0.000 ARG A 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6219 (mtm) cc_final: 0.5060 (mmp) REVERT: A 256 TYR cc_start: 0.6420 (t80) cc_final: 0.6136 (t80) REVERT: A 478 ASP cc_start: 0.7246 (t0) cc_final: 0.6946 (t0) REVERT: A 515 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6576 (tp) REVERT: A 552 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: A 754 ARG cc_start: 0.7497 (ptp-110) cc_final: 0.5998 (ptt90) REVERT: A 768 LYS cc_start: 0.7075 (mtmt) cc_final: 0.6454 (mttt) REVERT: A 774 ARG cc_start: 0.6754 (mtp85) cc_final: 0.6128 (mtt-85) REVERT: A 840 GLN cc_start: 0.7271 (mt0) cc_final: 0.6500 (mp10) REVERT: A 848 SER cc_start: 0.8493 (p) cc_final: 0.8111 (t) REVERT: A 882 GLU cc_start: 0.5865 (pm20) cc_final: 0.5443 (mp0) REVERT: A 924 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: A 936 GLU cc_start: 0.6999 (tp30) cc_final: 0.6717 (mp0) REVERT: A 937 LYS cc_start: 0.7213 (ttpt) cc_final: 0.6831 (tptp) REVERT: A 1077 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7502 (mmm) outliers start: 19 outliers final: 7 residues processed: 111 average time/residue: 1.3296 time to fit residues: 156.9917 Evaluate side-chains 103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 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 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8767 Z= 0.165 Angle : 0.588 7.095 12066 Z= 0.279 Chirality : 0.041 0.216 1441 Planarity : 0.004 0.038 1340 Dihedral : 10.986 175.709 3198 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.83 % Allowed : 9.34 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.04 (0.28), residues: 921 helix: 1.96 (0.22), residues: 575 sheet: 0.22 (0.90), residues: 31 loop : 0.46 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.003 0.001 HIS A 428 PHE 0.013 0.001 PHE A 608 TYR 0.016 0.002 TYR A 467 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.6056 (mtm) cc_final: 0.4920 (mmp) REVERT: A 256 TYR cc_start: 0.6350 (t80) cc_final: 0.6096 (t80) REVERT: A 478 ASP cc_start: 0.7157 (t0) cc_final: 0.6896 (t0) REVERT: A 515 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6560 (tp) REVERT: A 552 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: A 593 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.7127 (t) REVERT: A 754 ARG cc_start: 0.7559 (ptp-110) cc_final: 0.6106 (ptt90) REVERT: A 768 LYS cc_start: 0.6923 (mtmt) cc_final: 0.6492 (mttp) REVERT: A 774 ARG cc_start: 0.6667 (mtp85) cc_final: 0.6381 (mtp85) REVERT: A 794 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: A 840 GLN cc_start: 0.7255 (mt0) cc_final: 0.6458 (mp10) REVERT: A 848 SER cc_start: 0.8520 (p) cc_final: 0.8164 (t) REVERT: A 882 GLU cc_start: 0.5980 (pm20) cc_final: 0.5610 (mp0) REVERT: A 924 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: A 936 GLU cc_start: 0.7007 (tp30) cc_final: 0.6733 (mp0) REVERT: A 937 LYS cc_start: 0.7252 (ttpt) cc_final: 0.6840 (tptp) REVERT: A 1077 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7495 (mmm) outliers start: 22 outliers final: 3 residues processed: 110 average time/residue: 1.2176 time to fit residues: 143.5156 Evaluate side-chains 104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1077 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8767 Z= 0.172 Angle : 0.586 7.043 12066 Z= 0.278 Chirality : 0.041 0.211 1441 Planarity : 0.004 0.039 1340 Dihedral : 10.878 175.595 3198 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.83 % Allowed : 9.58 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.02 (0.28), residues: 921 helix: 1.97 (0.22), residues: 575 sheet: 0.14 (0.88), residues: 31 loop : 0.40 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS A 332 PHE 0.014 0.001 PHE A 608 TYR 0.016 0.002 TYR A 467 ARG 0.002 0.000 ARG A 962 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5966 (mtm) cc_final: 0.4910 (mmp) REVERT: A 478 ASP cc_start: 0.6984 (t0) cc_final: 0.6768 (t0) REVERT: A 515 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6570 (tp) REVERT: A 552 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: A 593 SER cc_start: 0.7420 (OUTLIER) cc_final: 0.7148 (t) REVERT: A 754 ARG cc_start: 0.7563 (ptp-110) cc_final: 0.6121 (ptt90) REVERT: A 768 LYS cc_start: 0.6984 (mtmt) cc_final: 0.6758 (mttp) REVERT: A 774 ARG cc_start: 0.6632 (mtp85) cc_final: 0.6220 (mtp-110) REVERT: A 794 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6836 (pp20) REVERT: A 840 GLN cc_start: 0.7263 (mt0) cc_final: 0.6458 (mp10) REVERT: A 846 PHE cc_start: 0.7204 (m-80) cc_final: 0.6941 (m-80) REVERT: A 882 GLU cc_start: 0.6120 (pm20) cc_final: 0.5735 (mp0) REVERT: A 924 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: A 936 GLU cc_start: 0.6989 (tp30) cc_final: 0.6716 (mp0) REVERT: A 937 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6855 (tptp) REVERT: A 1077 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7496 (mmm) outliers start: 22 outliers final: 5 residues processed: 108 average time/residue: 1.2960 time to fit residues: 149.4015 Evaluate side-chains 104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 21 optimal weight: 0.0270 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8767 Z= 0.149 Angle : 0.569 9.086 12066 Z= 0.267 Chirality : 0.040 0.209 1441 Planarity : 0.004 0.046 1340 Dihedral : 10.683 175.323 3198 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.32 % Allowed : 9.21 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.10 (0.28), residues: 921 helix: 2.07 (0.22), residues: 575 sheet: 0.15 (0.87), residues: 31 loop : 0.34 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS A 428 PHE 0.011 0.001 PHE A 608 TYR 0.015 0.001 TYR A 256 ARG 0.002 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5970 (mtm) cc_final: 0.4915 (mmp) REVERT: A 515 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6555 (tp) REVERT: A 552 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: A 593 SER cc_start: 0.7398 (OUTLIER) cc_final: 0.7120 (t) REVERT: A 754 ARG cc_start: 0.7558 (ptp-110) cc_final: 0.6095 (ptt90) REVERT: A 774 ARG cc_start: 0.6630 (mtp85) cc_final: 0.6305 (mtp-110) REVERT: A 794 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: A 840 GLN cc_start: 0.7245 (mt0) cc_final: 0.6439 (mp10) REVERT: A 846 PHE cc_start: 0.7234 (m-80) cc_final: 0.6995 (m-80) REVERT: A 848 SER cc_start: 0.8460 (p) cc_final: 0.8086 (t) REVERT: A 882 GLU cc_start: 0.6088 (pm20) cc_final: 0.5689 (mp0) REVERT: A 924 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6838 (tt0) REVERT: A 936 GLU cc_start: 0.6884 (tp30) cc_final: 0.6606 (mp0) REVERT: A 937 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6871 (mtmt) REVERT: A 1077 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7483 (mmm) REVERT: A 1111 MET cc_start: 0.8202 (mtm) cc_final: 0.7825 (mtm) outliers start: 26 outliers final: 11 residues processed: 108 average time/residue: 1.2897 time to fit residues: 148.5860 Evaluate side-chains 107 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1114 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8767 Z= 0.157 Angle : 0.570 8.254 12066 Z= 0.270 Chirality : 0.040 0.207 1441 Planarity : 0.004 0.038 1340 Dihedral : 10.486 176.509 3198 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.07 % Allowed : 10.20 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.06 (0.28), residues: 921 helix: 2.07 (0.22), residues: 575 sheet: 0.14 (0.88), residues: 31 loop : 0.28 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.002 0.001 HIS A 332 PHE 0.012 0.001 PHE A 608 TYR 0.017 0.001 TYR A 256 ARG 0.011 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5995 (mtm) cc_final: 0.4951 (mmp) REVERT: A 256 TYR cc_start: 0.6466 (t80) cc_final: 0.6217 (t80) REVERT: A 472 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6737 (tm-30) REVERT: A 515 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6590 (tp) REVERT: A 552 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: A 593 SER cc_start: 0.7372 (OUTLIER) cc_final: 0.7099 (t) REVERT: A 754 ARG cc_start: 0.7570 (ptp-110) cc_final: 0.6124 (ptt90) REVERT: A 774 ARG cc_start: 0.6630 (mtp85) cc_final: 0.6327 (mtp-110) REVERT: A 833 ARG cc_start: 0.7469 (mtt-85) cc_final: 0.7263 (mtm-85) REVERT: A 840 GLN cc_start: 0.7276 (mt0) cc_final: 0.6466 (mp10) REVERT: A 848 SER cc_start: 0.8459 (p) cc_final: 0.8080 (t) REVERT: A 882 GLU cc_start: 0.6022 (pm20) cc_final: 0.5676 (mp0) REVERT: A 924 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: A 936 GLU cc_start: 0.6863 (tp30) cc_final: 0.6589 (mp0) REVERT: A 937 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6868 (mtmt) REVERT: A 986 MET cc_start: 0.7505 (mmm) cc_final: 0.7299 (tpt) REVERT: A 1077 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7486 (mmm) REVERT: A 1111 MET cc_start: 0.8211 (mtm) cc_final: 0.7833 (mtm) outliers start: 24 outliers final: 10 residues processed: 105 average time/residue: 1.4324 time to fit residues: 159.8974 Evaluate side-chains 107 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1077 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8767 Z= 0.197 Angle : 0.598 9.491 12066 Z= 0.285 Chirality : 0.041 0.211 1441 Planarity : 0.004 0.038 1340 Dihedral : 10.685 174.637 3198 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.83 % Allowed : 10.44 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.95 (0.28), residues: 921 helix: 1.99 (0.22), residues: 573 sheet: 0.07 (0.87), residues: 31 loop : 0.22 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 650 HIS 0.003 0.001 HIS A 332 PHE 0.014 0.001 PHE A 608 TYR 0.016 0.002 TYR A 256 ARG 0.009 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5950 (mtm) cc_final: 0.4935 (mmp) REVERT: A 472 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: A 515 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6631 (tp) REVERT: A 552 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 593 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.7139 (t) REVERT: A 698 GLU cc_start: 0.6791 (tp30) cc_final: 0.6282 (pp20) REVERT: A 754 ARG cc_start: 0.7575 (ptp-110) cc_final: 0.6156 (ptt90) REVERT: A 774 ARG cc_start: 0.6660 (mtp85) cc_final: 0.6421 (mtp-110) REVERT: A 840 GLN cc_start: 0.7316 (mt0) cc_final: 0.6501 (mp10) REVERT: A 882 GLU cc_start: 0.6099 (pm20) cc_final: 0.5701 (mp0) REVERT: A 924 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: A 936 GLU cc_start: 0.6887 (tp30) cc_final: 0.6601 (mp0) REVERT: A 937 LYS cc_start: 0.7231 (ttpt) cc_final: 0.6817 (tptp) REVERT: A 1077 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7502 (mmm) REVERT: A 1111 MET cc_start: 0.8295 (mtm) cc_final: 0.7928 (mtm) outliers start: 22 outliers final: 12 residues processed: 108 average time/residue: 1.3462 time to fit residues: 155.2568 Evaluate side-chains 111 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1114 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8767 Z= 0.166 Angle : 0.585 10.956 12066 Z= 0.275 Chirality : 0.040 0.208 1441 Planarity : 0.004 0.038 1340 Dihedral : 10.585 173.965 3198 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.70 % Allowed : 10.57 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.96 (0.28), residues: 921 helix: 2.00 (0.22), residues: 575 sheet: 0.13 (0.88), residues: 31 loop : 0.20 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS A 332 PHE 0.011 0.001 PHE A 608 TYR 0.016 0.001 TYR A 256 ARG 0.009 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5999 (mtm) cc_final: 0.4969 (mmp) REVERT: A 472 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: A 515 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6573 (tp) REVERT: A 552 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: A 593 SER cc_start: 0.7398 (OUTLIER) cc_final: 0.7137 (t) REVERT: A 698 GLU cc_start: 0.6920 (tp30) cc_final: 0.6384 (pp20) REVERT: A 774 ARG cc_start: 0.6619 (mtp85) cc_final: 0.6413 (mtp-110) REVERT: A 840 GLN cc_start: 0.7284 (mt0) cc_final: 0.6471 (mp10) REVERT: A 858 MET cc_start: 0.7690 (tpp) cc_final: 0.7027 (mmt) REVERT: A 882 GLU cc_start: 0.6065 (pm20) cc_final: 0.5696 (mp0) REVERT: A 924 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 936 GLU cc_start: 0.6844 (tp30) cc_final: 0.6559 (mp0) REVERT: A 937 LYS cc_start: 0.7216 (ttpt) cc_final: 0.6865 (mtmt) REVERT: A 1011 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6483 (pp) outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 1.3115 time to fit residues: 141.6310 Evaluate side-chains 107 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1114 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8767 Z= 0.159 Angle : 0.579 12.136 12066 Z= 0.272 Chirality : 0.040 0.207 1441 Planarity : 0.004 0.038 1340 Dihedral : 10.528 172.905 3198 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.21 % Allowed : 10.93 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.99 (0.28), residues: 921 helix: 2.03 (0.22), residues: 575 sheet: 0.18 (0.88), residues: 31 loop : 0.18 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 650 HIS 0.002 0.001 HIS A 332 PHE 0.011 0.001 PHE A 608 TYR 0.016 0.001 TYR A 256 ARG 0.009 0.001 ARG A 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5944 (mtm) cc_final: 0.4940 (mmp) REVERT: A 472 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: A 515 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6587 (tp) REVERT: A 552 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: A 593 SER cc_start: 0.7380 (OUTLIER) cc_final: 0.7112 (t) REVERT: A 698 GLU cc_start: 0.6857 (tp30) cc_final: 0.6344 (pp20) REVERT: A 840 GLN cc_start: 0.7281 (mt0) cc_final: 0.6462 (mp10) REVERT: A 858 MET cc_start: 0.7719 (tpp) cc_final: 0.7516 (mmt) REVERT: A 882 GLU cc_start: 0.6052 (pm20) cc_final: 0.5729 (mp0) REVERT: A 924 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: A 936 GLU cc_start: 0.6836 (tp30) cc_final: 0.6556 (mp0) REVERT: A 937 LYS cc_start: 0.7211 (ttpt) cc_final: 0.6868 (mtmt) REVERT: A 1011 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6485 (pp) REVERT: A 1111 MET cc_start: 0.8203 (mtm) cc_final: 0.7829 (mtm) outliers start: 17 outliers final: 11 residues processed: 98 average time/residue: 1.2576 time to fit residues: 131.9724 Evaluate side-chains 106 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1114 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.0030 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136088 restraints weight = 18133.216| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.10 r_work: 0.3383 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8767 Z= 0.154 Angle : 0.575 12.516 12066 Z= 0.269 Chirality : 0.040 0.207 1441 Planarity : 0.004 0.038 1340 Dihedral : 10.490 172.213 3198 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.33 % Allowed : 11.06 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.01 (0.28), residues: 921 helix: 2.05 (0.22), residues: 576 sheet: 0.20 (0.89), residues: 31 loop : 0.19 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 650 HIS 0.002 0.001 HIS A 332 PHE 0.011 0.001 PHE A 608 TYR 0.017 0.001 TYR A 256 ARG 0.009 0.000 ARG A 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.71 seconds wall clock time: 58 minutes 53.18 seconds (3533.18 seconds total)