Starting phenix.real_space_refine on Mon Dec 30 04:11:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ajm_15484/12_2024/8ajm_15484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ajm_15484/12_2024/8ajm_15484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ajm_15484/12_2024/8ajm_15484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ajm_15484/12_2024/8ajm_15484.map" model { file = "/net/cci-nas-00/data/ceres_data/8ajm_15484/12_2024/8ajm_15484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ajm_15484/12_2024/8ajm_15484.cif" } resolution = 2.83 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= 0.002 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7656 2.51 5 N 2063 2.21 5 O 2327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12106 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8918 Classifications: {'peptide': 1140} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 1098} Chain: "B" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3131 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 377} Chain breaks: 2 Chain: "C" Number of atoms: 57 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 5, 38 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Conformer: "B" Number of residues, atoms: 5, 38 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} bond proxies already assigned to first conformer: 18 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLU C 540 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU C 540 " occ=0.50 residue: pdb=" N AGLU C 541 " occ=0.70 ... (18 atoms not shown) pdb=" OXTBGLU C 541 " occ=0.30 Time building chain proxies: 7.17, per 1000 atoms: 0.59 Number of scatterers: 12106 At special positions: 0 Unit cell: (109.22, 95.46, 147.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2327 8.00 N 2063 7.00 C 7656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 313 " distance=2.03 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: 3.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 33 sheets defined 7.9% alpha, 43.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 1044 through 1059 Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1091 through 1095 Processing helix chain 'A' and resid 1096 through 1099 Processing helix chain 'A' and resid 1101 through 1110 removed outlier: 3.721A pdb=" N GLU A1107 " --> pdb=" O PRO A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1137 removed outlier: 3.809A pdb=" N LEU A1129 " --> pdb=" O THR A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1140 No H-bonds generated for 'chain 'A' and resid 1138 through 1140' Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.524A pdb=" N TYR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'B' and resid 404 through 411 Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009 removed outlier: 3.517A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLY A1026 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER A1042 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 5.975A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.263A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA A 86 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS A 105 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 88 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.257A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 166 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169 removed outlier: 6.257A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 166 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 218 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263 removed outlier: 3.587A pdb=" N CYS A 260 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU A 280 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU A 304 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET A 282 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 302 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 284 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU A 300 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU A 286 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 313 through 318 removed outlier: 6.611A pdb=" N VAL A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ALA A 349 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 365 removed outlier: 3.791A pdb=" N ASP A 361 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 396 through 402 removed outlier: 6.950A pdb=" N ILE A 701 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A 401 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 699 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AB4, first strand: chain 'A' and resid 457 through 463 removed outlier: 5.964A pdb=" N SER A 480 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A 486 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.607A pdb=" N VAL A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 516 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS A 531 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TYR A 518 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.332A pdb=" N GLY A 559 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 541 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 557 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A 565 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 578 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 570 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A 576 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 588 through 596 removed outlier: 3.572A pdb=" N SER A 590 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS A 600 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 611 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS A 628 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A 613 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG A 626 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 637 through 643 removed outlier: 8.440A pdb=" N THR A 647 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER A 661 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.057A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 720 through 727 removed outlier: 6.057A pdb=" N SER A 738 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 723 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER A 764 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 811 through 820 removed outlier: 6.637A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR A 827 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR A 853 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY A 846 " --> pdb=" O GLU A 865 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU A 865 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 848 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU A 863 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 850 " --> pdb=" O VAL A 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 870 through 876 removed outlier: 3.698A pdb=" N SER A 872 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 888 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN A 904 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 890 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 911 through 917 removed outlier: 3.518A pdb=" N ALA A 946 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 934 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU A 944 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 954 through 959 removed outlier: 6.764A pdb=" N ALA A 968 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A 957 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 966 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE A 959 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASN A 964 " --> pdb=" O ILE A 959 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 996 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AC7, first strand: chain 'A' and resid 1113 through 1115 Processing sheet with id=AC8, first strand: chain 'B' and resid 81 through 83 removed outlier: 7.168A pdb=" N GLY B 438 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL B 421 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 97 removed outlier: 3.650A pdb=" N ALA B 94 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU B 112 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 146 through 148 removed outlier: 7.164A pdb=" N ILE B 167 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 174 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 190 through 192 Processing sheet with id=AD3, first strand: chain 'B' and resid 255 through 261 removed outlier: 4.121A pdb=" N TYR B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE B 276 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER B 290 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 278 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AD5, first strand: chain 'B' and resid 343 through 349 removed outlier: 3.793A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 343 through 349 removed outlier: 3.793A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1254 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: 6.27 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3514 1.33 - 1.45: 2237 1.45 - 1.58: 6508 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 12348 Sorted by residual: bond pdb=" CA LEU B 57 " pdb=" C LEU B 57 " ideal model delta sigma weight residual 1.531 1.512 0.019 1.12e-02 7.97e+03 2.84e+00 bond pdb=" CB ARG A 947 " pdb=" CG ARG A 947 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" CB TYR A1048 " pdb=" CG TYR A1048 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.20e-02 2.07e+03 2.34e+00 bond pdb=" CG ARG A1074 " pdb=" CD ARG A1074 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CG PRO A 843 " pdb=" CD PRO A 843 " ideal model delta sigma weight residual 1.503 1.452 0.051 3.40e-02 8.65e+02 2.27e+00 ... (remaining 12343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 14826 1.25 - 2.49: 1648 2.49 - 3.74: 218 3.74 - 4.99: 39 4.99 - 6.23: 8 Bond angle restraints: 16739 Sorted by residual: angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.28 123.18 -3.90 1.10e+00 8.26e-01 1.26e+01 angle pdb=" C GLU C 538 " pdb=" CA GLU C 538 " pdb=" CB GLU C 538 " ideal model delta sigma weight residual 111.83 106.77 5.06 1.60e+00 3.91e-01 1.00e+01 angle pdb=" CA TRP A1073 " pdb=" CB TRP A1073 " pdb=" CG TRP A1073 " ideal model delta sigma weight residual 113.60 119.52 -5.92 1.90e+00 2.77e-01 9.70e+00 angle pdb=" CA TRP B 308 " pdb=" CB TRP B 308 " pdb=" CG TRP B 308 " ideal model delta sigma weight residual 113.60 107.72 5.88 1.90e+00 2.77e-01 9.57e+00 angle pdb=" CA TRP A 207 " pdb=" CB TRP A 207 " pdb=" CG TRP A 207 " ideal model delta sigma weight residual 113.60 119.21 -5.61 1.90e+00 2.77e-01 8.71e+00 ... (remaining 16734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7049 17.91 - 35.83: 279 35.83 - 53.74: 54 53.74 - 71.65: 20 71.65 - 89.57: 9 Dihedral angle restraints: 7411 sinusoidal: 2962 harmonic: 4449 Sorted by residual: dihedral pdb=" CA VAL B 178 " pdb=" C VAL B 178 " pdb=" N GLY B 179 " pdb=" CA GLY B 179 " ideal model delta harmonic sigma weight residual 180.00 153.51 26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CB CYS A 18 " pdb=" SG CYS A 18 " pdb=" SG CYS A 313 " pdb=" CB CYS A 313 " ideal model delta sinusoidal sigma weight residual 93.00 135.51 -42.51 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CA TYR B 232 " pdb=" C TYR B 232 " pdb=" N ALA B 233 " pdb=" CA ALA B 233 " ideal model delta harmonic sigma weight residual 180.00 155.52 24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 7408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1316 0.070 - 0.140: 465 0.140 - 0.210: 102 0.210 - 0.280: 11 0.280 - 0.350: 4 Chirality restraints: 1898 Sorted by residual: chirality pdb=" CA TYR A 84 " pdb=" N TYR A 84 " pdb=" C TYR A 84 " pdb=" CB TYR A 84 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA SER A 645 " pdb=" N SER A 645 " pdb=" C SER A 645 " pdb=" CB SER A 645 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PHE A 799 " pdb=" N PHE A 799 " pdb=" C PHE A 799 " pdb=" CB PHE A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1895 not shown) Planarity restraints: 2165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 308 " 0.053 2.00e-02 2.50e+03 2.45e-02 1.49e+01 pdb=" CG TRP B 308 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 308 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 308 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP B 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 308 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 308 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 308 " 0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 308 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 308 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 998 " -0.038 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE A 998 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 998 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 998 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 998 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 998 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 998 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 210 " 0.035 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP B 210 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 210 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 210 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 210 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 210 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 210 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 210 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 210 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 210 " 0.020 2.00e-02 2.50e+03 ... (remaining 2162 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2437 2.78 - 3.31: 10566 3.31 - 3.84: 20140 3.84 - 4.37: 24615 4.37 - 4.90: 42388 Nonbonded interactions: 100146 Sorted by model distance: nonbonded pdb=" OG SER B 271 " pdb=" OD1 ASP B 273 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP A 125 " pdb=" N ARG A 129 " model vdw 2.329 3.120 nonbonded pdb=" O LEU A1093 " pdb=" OG SER A1096 " model vdw 2.333 3.040 nonbonded pdb=" OG SER A 256 " pdb=" NH2 ARG A 279 " model vdw 2.377 3.120 nonbonded pdb=" O ASN B 110 " pdb=" ND2 ASN B 110 " model vdw 2.381 3.120 ... (remaining 100141 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=0.00 max=1.00 mean=0.87 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: 1.320 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 32.710 Find NCS groups from input model: 0.140 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:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.008 0.051 12348 Z= 0.535 Angle : 0.825 6.233 16739 Z= 0.497 Chirality : 0.073 0.350 1898 Planarity : 0.006 0.082 2165 Dihedral : 11.452 89.568 4548 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.52 % Allowed : 2.45 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: 0.01 (0.20), residues: 1532 helix: -0.84 (0.46), residues: 102 sheet: 0.35 (0.19), residues: 673 loop : -0.05 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.006 TRP B 308 HIS 0.010 0.001 HIS B 445 PHE 0.052 0.005 PHE A 998 TYR 0.035 0.004 TYR A 239 ARG 0.005 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.419 Fit side-chains REVERT: A 782 PHE cc_start: 0.8089 (t80) cc_final: 0.7662 (t80) REVERT: B 109 CYS cc_start: 0.7869 (t) cc_final: 0.7574 (t) outliers start: 7 outliers final: 2 residues processed: 146 average time/residue: 1.7127 time to fit residues: 267.8644 Evaluate side-chains 59 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain B residue 55 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 105 HIS B 110 ASN B 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12348 Z= 0.374 Angle : 0.653 8.926 16739 Z= 0.351 Chirality : 0.048 0.156 1898 Planarity : 0.004 0.045 2165 Dihedral : 5.471 39.777 1666 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.37 % Allowed : 6.82 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: 0.03 (0.21), residues: 1532 helix: -0.07 (0.49), residues: 111 sheet: 0.38 (0.19), residues: 686 loop : -0.19 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 561 HIS 0.005 0.001 HIS B 445 PHE 0.029 0.002 PHE A 998 TYR 0.017 0.002 TYR A 193 ARG 0.008 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 350 MET cc_start: 0.8301 (mtp) cc_final: 0.8033 (mtm) REVERT: A 782 PHE cc_start: 0.8121 (t80) cc_final: 0.7779 (t80) outliers start: 32 outliers final: 8 residues processed: 92 average time/residue: 1.5505 time to fit residues: 154.1988 Evaluate side-chains 56 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 539 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 50.0000 chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 47 optimal weight: 50.0000 chunk 111 optimal weight: 0.0030 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 HIS B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12348 Z= 0.238 Angle : 0.568 8.063 16739 Z= 0.303 Chirality : 0.046 0.153 1898 Planarity : 0.004 0.039 2165 Dihedral : 4.944 26.256 1665 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.85 % Allowed : 7.78 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.05 (0.21), residues: 1532 helix: 0.25 (0.49), residues: 113 sheet: 0.29 (0.19), residues: 686 loop : -0.28 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 561 HIS 0.004 0.001 HIS B 445 PHE 0.017 0.002 PHE A 998 TYR 0.014 0.001 TYR A 193 ARG 0.010 0.000 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 1.667 Fit side-chains REVERT: A 782 PHE cc_start: 0.8081 (t80) cc_final: 0.7845 (t80) outliers start: 25 outliers final: 7 residues processed: 73 average time/residue: 1.6149 time to fit residues: 127.8971 Evaluate side-chains 54 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 539 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 950 ASN B 110 ASN B 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12348 Z= 0.294 Angle : 0.579 8.833 16739 Z= 0.308 Chirality : 0.046 0.153 1898 Planarity : 0.004 0.051 2165 Dihedral : 4.910 32.181 1663 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.63 % Allowed : 8.82 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.21 (0.20), residues: 1532 helix: 0.34 (0.49), residues: 114 sheet: 0.15 (0.19), residues: 682 loop : -0.39 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 561 HIS 0.004 0.001 HIS B 445 PHE 0.021 0.002 PHE A 998 TYR 0.014 0.001 TYR A 193 ARG 0.010 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 1.430 Fit side-chains REVERT: A 782 PHE cc_start: 0.8094 (t80) cc_final: 0.7824 (t80) outliers start: 22 outliers final: 12 residues processed: 68 average time/residue: 1.4824 time to fit residues: 110.0971 Evaluate side-chains 58 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 539 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 50.0000 chunk 126 optimal weight: 0.0040 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN A 908 ASN B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12348 Z= 0.150 Angle : 0.513 9.489 16739 Z= 0.274 Chirality : 0.045 0.154 1898 Planarity : 0.003 0.046 2165 Dihedral : 4.528 34.408 1663 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.41 % Allowed : 9.41 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.09 (0.21), residues: 1532 helix: 0.63 (0.49), residues: 114 sheet: 0.18 (0.19), residues: 705 loop : -0.29 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 561 HIS 0.004 0.001 HIS B 445 PHE 0.013 0.001 PHE A1030 TYR 0.012 0.001 TYR A 42 ARG 0.010 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 782 PHE cc_start: 0.8012 (t80) cc_final: 0.7773 (t80) outliers start: 19 outliers final: 7 residues processed: 71 average time/residue: 1.4340 time to fit residues: 111.3702 Evaluate side-chains 53 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 334 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 203 ASN B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 12348 Z= 0.536 Angle : 0.680 10.330 16739 Z= 0.355 Chirality : 0.049 0.184 1898 Planarity : 0.005 0.065 2165 Dihedral : 5.287 47.469 1663 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.30 % Allowed : 9.93 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.50 (0.20), residues: 1532 helix: 0.33 (0.49), residues: 112 sheet: 0.01 (0.19), residues: 680 loop : -0.68 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 207 HIS 0.008 0.001 HIS B 445 PHE 0.028 0.002 PHE A 998 TYR 0.017 0.002 TYR A 193 ARG 0.011 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 50 time to evaluate : 1.459 Fit side-chains REVERT: A 782 PHE cc_start: 0.8178 (t80) cc_final: 0.7869 (t80) outliers start: 31 outliers final: 13 residues processed: 76 average time/residue: 1.3687 time to fit residues: 114.4684 Evaluate side-chains 62 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 147 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 50.0000 chunk 91 optimal weight: 1.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12348 Z= 0.217 Angle : 0.558 10.696 16739 Z= 0.293 Chirality : 0.046 0.179 1898 Planarity : 0.004 0.057 2165 Dihedral : 4.895 47.354 1663 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.70 % Allowed : 10.90 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.40 (0.20), residues: 1532 helix: 0.44 (0.49), residues: 114 sheet: 0.08 (0.19), residues: 674 loop : -0.62 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 207 HIS 0.006 0.001 HIS A 397 PHE 0.018 0.002 PHE A 998 TYR 0.012 0.001 TYR A 42 ARG 0.012 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 2.223 Fit side-chains REVERT: A 782 PHE cc_start: 0.8089 (t80) cc_final: 0.7849 (t80) outliers start: 23 outliers final: 11 residues processed: 68 average time/residue: 1.5274 time to fit residues: 115.0109 Evaluate side-chains 57 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12348 Z= 0.218 Angle : 0.565 11.321 16739 Z= 0.294 Chirality : 0.045 0.152 1898 Planarity : 0.004 0.063 2165 Dihedral : 4.776 47.778 1663 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.26 % Allowed : 11.34 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.40 (0.21), residues: 1532 helix: 0.49 (0.49), residues: 114 sheet: 0.05 (0.19), residues: 681 loop : -0.60 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 207 HIS 0.005 0.001 HIS A 397 PHE 0.018 0.002 PHE A 998 TYR 0.012 0.001 TYR A 193 ARG 0.012 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 1.787 Fit side-chains REVERT: A 782 PHE cc_start: 0.8073 (t80) cc_final: 0.7773 (t80) outliers start: 17 outliers final: 8 residues processed: 64 average time/residue: 1.3708 time to fit residues: 96.7186 Evaluate side-chains 53 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12348 Z= 0.334 Angle : 0.612 11.724 16739 Z= 0.316 Chirality : 0.047 0.254 1898 Planarity : 0.004 0.062 2165 Dihedral : 4.967 48.865 1663 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.33 % Allowed : 11.42 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.50 (0.21), residues: 1532 helix: 0.41 (0.49), residues: 114 sheet: -0.04 (0.19), residues: 677 loop : -0.64 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 561 HIS 0.005 0.001 HIS B 445 PHE 0.022 0.002 PHE A 998 TYR 0.012 0.001 TYR A 193 ARG 0.007 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 1.436 Fit side-chains REVERT: A 782 PHE cc_start: 0.8146 (t80) cc_final: 0.7916 (t80) REVERT: A 1120 MET cc_start: 0.3647 (ppp) cc_final: 0.3352 (pp-130) outliers start: 18 outliers final: 11 residues processed: 58 average time/residue: 1.4259 time to fit residues: 91.0928 Evaluate side-chains 54 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 50.0000 chunk 101 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12348 Z= 0.211 Angle : 0.584 11.432 16739 Z= 0.301 Chirality : 0.046 0.222 1898 Planarity : 0.004 0.063 2165 Dihedral : 4.775 48.185 1663 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.89 % Allowed : 11.93 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.44 (0.21), residues: 1532 helix: 0.54 (0.49), residues: 114 sheet: 0.02 (0.19), residues: 682 loop : -0.63 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 561 HIS 0.004 0.001 HIS A 397 PHE 0.016 0.002 PHE A 998 TYR 0.011 0.001 TYR A 193 ARG 0.007 0.000 ARG A 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 1.437 Fit side-chains REVERT: A 782 PHE cc_start: 0.8052 (t80) cc_final: 0.7750 (t80) REVERT: A 1120 MET cc_start: 0.3779 (ppp) cc_final: 0.3529 (pp-130) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 1.3210 time to fit residues: 83.5582 Evaluate side-chains 49 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 425 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 50 optimal weight: 40.0000 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.111699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072848 restraints weight = 66895.275| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.44 r_work: 0.3038 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12348 Z= 0.211 Angle : 0.573 11.010 16739 Z= 0.296 Chirality : 0.046 0.220 1898 Planarity : 0.004 0.062 2165 Dihedral : 4.696 48.459 1663 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.74 % Allowed : 12.16 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.40 (0.21), residues: 1532 helix: 0.67 (0.50), residues: 114 sheet: 0.05 (0.19), residues: 681 loop : -0.63 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 561 HIS 0.004 0.001 HIS B 445 PHE 0.016 0.002 PHE A 998 TYR 0.011 0.001 TYR A 193 ARG 0.007 0.000 ARG A 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3729.12 seconds wall clock time: 68 minutes 1.30 seconds (4081.30 seconds total)