Starting phenix.real_space_refine on Wed Jul 30 08:29:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ajm_15484/07_2025/8ajm_15484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ajm_15484/07_2025/8ajm_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_15484/07_2025/8ajm_15484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ajm_15484/07_2025/8ajm_15484.map" model { file = "/net/cci-nas-00/data/ceres_data/8ajm_15484/07_2025/8ajm_15484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ajm_15484/07_2025/8ajm_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-5711/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: 7.21, per 1000 atoms: 0.60 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: 2.67 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: 1.89 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: 5.93 Time building geometry restraints manager: 3.24 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: 48.880 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: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.890 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.620 ------------------------------------------------------------------------------- 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 12349 Z= 0.373 Angle : 0.825 6.233 16741 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 Details of bonding type rmsd hydrogen bonds : bond 0.17700 ( 447) hydrogen bonds : angle 8.47811 ( 1254) SS BOND : bond 0.00357 ( 1) SS BOND : angle 2.21030 ( 2) covalent geometry : bond 0.00813 (12348) covalent geometry : angle 0.82498 (16739) *********************** 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 : 1.524 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: 1.7010 time to fit residues: 266.4336 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 : 1.296 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.110754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072681 restraints weight = 62595.355| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.25 r_work: 0.3057 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 12349 Z= 0.252 Angle : 0.654 8.926 16741 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 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 447) hydrogen bonds : angle 6.20207 ( 1254) SS BOND : bond 0.00242 ( 1) SS BOND : angle 1.50285 ( 2) covalent geometry : bond 0.00567 (12348) covalent geometry : angle 0.65340 (16739) *********************** 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 : 1.319 Fit side-chains revert: symmetry clash REVERT: A 178 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7759 (mm) REVERT: A 350 MET cc_start: 0.8899 (mtp) cc_final: 0.8600 (mtm) REVERT: A 782 PHE cc_start: 0.8142 (t80) cc_final: 0.7673 (t80) REVERT: A 896 GLU cc_start: 0.8963 (mp0) cc_final: 0.8705 (pm20) REVERT: A 1062 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8322 (pp) REVERT: B 109 CYS cc_start: 0.8391 (t) cc_final: 0.8060 (t) REVERT: B 288 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8274 (mp) outliers start: 32 outliers final: 8 residues processed: 92 average time/residue: 1.4667 time to fit residues: 145.9669 Evaluate side-chains 61 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 1062 ILE 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 288 LEU 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 30 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 40.0000 chunk 69 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.110602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.072317 restraints weight = 45431.097| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.76 r_work: 0.3064 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12349 Z= 0.218 Angle : 0.600 7.824 16741 Z= 0.320 Chirality : 0.047 0.158 1898 Planarity : 0.004 0.042 2165 Dihedral : 5.163 28.479 1665 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.00 % Allowed : 7.93 % Favored : 90.07 % 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: -0.17 (0.21), residues: 1532 helix: 0.14 (0.49), residues: 113 sheet: 0.21 (0.19), residues: 687 loop : -0.35 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 561 HIS 0.005 0.001 HIS B 445 PHE 0.023 0.002 PHE A 998 TYR 0.016 0.002 TYR A 193 ARG 0.010 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 447) hydrogen bonds : angle 5.86820 ( 1254) SS BOND : bond 0.00293 ( 1) SS BOND : angle 1.04861 ( 2) covalent geometry : bond 0.00491 (12348) covalent geometry : angle 0.60027 (16739) *********************** 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 82 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 1.750 Fit side-chains REVERT: A 178 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7713 (mm) REVERT: A 350 MET cc_start: 0.8730 (mtp) cc_final: 0.8376 (mtm) REVERT: A 782 PHE cc_start: 0.8124 (t80) cc_final: 0.7696 (t80) REVERT: A 896 GLU cc_start: 0.8855 (mp0) cc_final: 0.8628 (pm20) REVERT: A 990 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8420 (mp10) REVERT: A 1062 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8405 (pp) REVERT: A 1120 MET cc_start: 0.7314 (pp-130) cc_final: 0.7051 (ppp) REVERT: B 109 CYS cc_start: 0.8485 (t) cc_final: 0.8161 (t) outliers start: 27 outliers final: 10 residues processed: 76 average time/residue: 1.6959 time to fit residues: 140.9990 Evaluate side-chains 63 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 761 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 990 GLN Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 207 MET 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 130 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 149 optimal weight: 0.0870 chunk 116 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.112991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.074890 restraints weight = 51341.132| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.01 r_work: 0.3107 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12349 Z= 0.111 Angle : 0.524 7.114 16741 Z= 0.280 Chirality : 0.045 0.152 1898 Planarity : 0.004 0.041 2165 Dihedral : 4.648 30.526 1663 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.70 % Allowed : 8.52 % Favored : 89.77 % 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: -0.10 (0.20), residues: 1532 helix: 0.31 (0.49), residues: 116 sheet: 0.24 (0.19), residues: 689 loop : -0.31 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 561 HIS 0.006 0.001 HIS A 536 PHE 0.013 0.001 PHE A1030 TYR 0.013 0.001 TYR A 42 ARG 0.010 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 447) hydrogen bonds : angle 5.40917 ( 1254) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.84081 ( 2) covalent geometry : bond 0.00246 (12348) covalent geometry : angle 0.52349 (16739) *********************** 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 79 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 1.309 Fit side-chains REVERT: A 178 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7746 (mm) REVERT: A 782 PHE cc_start: 0.8068 (t80) cc_final: 0.7629 (t80) REVERT: A 1054 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8094 (mtm) REVERT: A 1062 ILE cc_start: 0.8624 (tt) cc_final: 0.8284 (pp) REVERT: A 1120 MET cc_start: 0.7164 (pp-130) cc_final: 0.6948 (ppp) outliers start: 23 outliers final: 9 residues processed: 74 average time/residue: 1.3540 time to fit residues: 109.4777 Evaluate side-chains 56 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 768 SER Chi-restraints excluded: chain A residue 1054 MET 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 34 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 5 optimal weight: 0.0170 chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 131 optimal weight: 30.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.110915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.072298 restraints weight = 57977.547| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.14 r_work: 0.3028 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 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 = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12349 Z= 0.212 Angle : 0.567 6.193 16741 Z= 0.302 Chirality : 0.046 0.152 1898 Planarity : 0.004 0.053 2165 Dihedral : 4.905 39.373 1663 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.85 % Allowed : 8.82 % Favored : 89.33 % 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: -0.30 (0.20), residues: 1532 helix: 0.26 (0.49), residues: 116 sheet: 0.11 (0.19), residues: 679 loop : -0.47 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 561 HIS 0.006 0.001 HIS B 445 PHE 0.023 0.002 PHE A 998 TYR 0.015 0.002 TYR A 193 ARG 0.011 0.001 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 447) hydrogen bonds : angle 5.63684 ( 1254) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.78861 ( 2) covalent geometry : bond 0.00481 (12348) covalent geometry : angle 0.56732 (16739) *********************** 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 77 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 1.322 Fit side-chains REVERT: A 178 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7606 (tp) REVERT: A 350 MET cc_start: 0.8797 (mtp) cc_final: 0.8584 (mtm) REVERT: A 782 PHE cc_start: 0.8162 (t80) cc_final: 0.7813 (t80) REVERT: A 1062 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8382 (pp) REVERT: A 1120 MET cc_start: 0.7269 (pp-130) cc_final: 0.7024 (pp-130) outliers start: 25 outliers final: 12 residues processed: 71 average time/residue: 1.3078 time to fit residues: 102.1511 Evaluate side-chains 60 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 768 SER Chi-restraints excluded: chain A residue 1062 ILE 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 Chi-restraints excluded: chain C residue 539 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.110478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.072595 restraints weight = 45103.703| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.73 r_work: 0.3040 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12349 Z= 0.224 Angle : 0.583 7.893 16741 Z= 0.307 Chirality : 0.046 0.153 1898 Planarity : 0.004 0.055 2165 Dihedral : 4.990 45.890 1663 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.37 % Allowed : 9.56 % Favored : 88.07 % 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: -0.42 (0.20), residues: 1532 helix: 0.28 (0.49), residues: 116 sheet: 0.07 (0.19), residues: 674 loop : -0.60 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 561 HIS 0.005 0.001 HIS B 445 PHE 0.021 0.002 PHE A 998 TYR 0.014 0.002 TYR A 193 ARG 0.011 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 447) hydrogen bonds : angle 5.65777 ( 1254) SS BOND : bond 0.00292 ( 1) SS BOND : angle 0.80016 ( 2) covalent geometry : bond 0.00507 (12348) covalent geometry : angle 0.58314 (16739) *********************** 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 83 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 51 time to evaluate : 1.373 Fit side-chains REVERT: A 178 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7756 (mm) REVERT: A 350 MET cc_start: 0.8716 (mtp) cc_final: 0.8488 (mtm) REVERT: A 782 PHE cc_start: 0.8144 (t80) cc_final: 0.7772 (t80) REVERT: A 994 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: A 1120 MET cc_start: 0.7320 (pp-130) cc_final: 0.7068 (pp-130) outliers start: 32 outliers final: 14 residues processed: 76 average time/residue: 1.3495 time to fit residues: 112.6846 Evaluate side-chains 63 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 768 SER Chi-restraints excluded: chain A residue 994 GLU 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 232 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain C residue 539 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 39 optimal weight: 0.0070 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 127 optimal weight: 9.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.111049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072921 restraints weight = 47722.922| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.83 r_work: 0.3053 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12349 Z= 0.171 Angle : 0.575 8.485 16741 Z= 0.300 Chirality : 0.046 0.157 1898 Planarity : 0.004 0.056 2165 Dihedral : 4.869 47.164 1663 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.22 % Allowed : 9.64 % Favored : 88.14 % 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: -0.45 (0.20), residues: 1532 helix: 0.31 (0.48), residues: 116 sheet: 0.01 (0.19), residues: 677 loop : -0.60 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 561 HIS 0.005 0.001 HIS A 397 PHE 0.019 0.002 PHE A 998 TYR 0.012 0.001 TYR A 42 ARG 0.012 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 447) hydrogen bonds : angle 5.51836 ( 1254) SS BOND : bond 0.00294 ( 1) SS BOND : angle 0.79643 ( 2) covalent geometry : bond 0.00388 (12348) covalent geometry : angle 0.57493 (16739) *********************** 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 81 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 1.489 Fit side-chains REVERT: A 178 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7648 (tp) REVERT: A 350 MET cc_start: 0.8709 (mtp) cc_final: 0.8499 (mtm) REVERT: A 782 PHE cc_start: 0.8130 (t80) cc_final: 0.7806 (t80) REVERT: A 1120 MET cc_start: 0.7369 (pp-130) cc_final: 0.7115 (pp-130) outliers start: 30 outliers final: 13 residues processed: 75 average time/residue: 1.7434 time to fit residues: 143.5336 Evaluate side-chains 61 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 299 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 1109 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 50.0000 chunk 105 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.111047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.073003 restraints weight = 39046.242| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.55 r_work: 0.3068 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12349 Z= 0.179 Angle : 0.580 12.028 16741 Z= 0.302 Chirality : 0.046 0.154 1898 Planarity : 0.004 0.063 2165 Dihedral : 4.864 47.770 1663 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.93 % Allowed : 10.45 % Favored : 87.62 % 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: -0.49 (0.21), residues: 1532 helix: 0.31 (0.48), residues: 116 sheet: -0.02 (0.19), residues: 682 loop : -0.62 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 561 HIS 0.005 0.001 HIS B 445 PHE 0.019 0.002 PHE A 998 TYR 0.013 0.001 TYR A 193 ARG 0.013 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 447) hydrogen bonds : angle 5.53228 ( 1254) SS BOND : bond 0.00283 ( 1) SS BOND : angle 0.69476 ( 2) covalent geometry : bond 0.00406 (12348) covalent geometry : angle 0.58031 (16739) *********************** 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 76 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 1.746 Fit side-chains REVERT: A 178 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7663 (tp) REVERT: A 350 MET cc_start: 0.8667 (mtp) cc_final: 0.8462 (mtm) REVERT: A 782 PHE cc_start: 0.8135 (t80) cc_final: 0.7807 (t80) REVERT: A 910 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8250 (tmm) REVERT: A 1120 MET cc_start: 0.7396 (pp-130) cc_final: 0.7140 (pp-130) outliers start: 26 outliers final: 13 residues processed: 69 average time/residue: 1.4240 time to fit residues: 109.1846 Evaluate side-chains 61 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 252 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain C residue 539 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 8 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 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 908 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 = 0.4028 r_free = 0.4028 target = 0.111937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.074395 restraints weight = 50911.552| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.93 r_work: 0.3084 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12349 Z= 0.109 Angle : 0.546 9.314 16741 Z= 0.285 Chirality : 0.045 0.228 1898 Planarity : 0.003 0.062 2165 Dihedral : 4.625 46.717 1663 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.56 % Allowed : 11.05 % 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: -0.39 (0.21), residues: 1532 helix: 0.53 (0.49), residues: 116 sheet: 0.01 (0.19), residues: 688 loop : -0.55 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 561 HIS 0.004 0.001 HIS B 445 PHE 0.014 0.001 PHE A1030 TYR 0.012 0.001 TYR A 193 ARG 0.007 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 447) hydrogen bonds : angle 5.29740 ( 1254) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.70568 ( 2) covalent geometry : bond 0.00247 (12348) covalent geometry : angle 0.54564 (16739) *********************** 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 66 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 1.476 Fit side-chains REVERT: A 178 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 782 PHE cc_start: 0.8063 (t80) cc_final: 0.7671 (t80) REVERT: A 910 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8211 (tmm) REVERT: A 1120 MET cc_start: 0.7325 (pp-130) cc_final: 0.7060 (pp-130) REVERT: C 538 GLU cc_start: 0.7112 (tp30) cc_final: 0.6787 (tm-30) outliers start: 21 outliers final: 7 residues processed: 60 average time/residue: 1.6987 time to fit residues: 111.5726 Evaluate side-chains 52 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 252 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.111007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.072916 restraints weight = 53490.155| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.03 r_work: 0.3042 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 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 = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12349 Z= 0.179 Angle : 0.595 11.705 16741 Z= 0.306 Chirality : 0.046 0.240 1898 Planarity : 0.004 0.063 2165 Dihedral : 4.768 47.902 1663 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.96 % Allowed : 11.56 % Favored : 87.47 % 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: 0.50 (0.49), residues: 116 sheet: -0.02 (0.19), residues: 687 loop : -0.59 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 561 HIS 0.005 0.001 HIS B 445 PHE 0.019 0.002 PHE A 998 TYR 0.013 0.001 TYR A 193 ARG 0.008 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 447) hydrogen bonds : angle 5.47894 ( 1254) SS BOND : bond 0.00235 ( 1) SS BOND : angle 0.65897 ( 2) covalent geometry : bond 0.00408 (12348) covalent geometry : angle 0.59503 (16739) ********************** 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 57 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 1.339 Fit side-chains REVERT: A 178 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 782 PHE cc_start: 0.8123 (t80) cc_final: 0.7703 (t80) REVERT: A 910 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8282 (tmm) REVERT: A 1120 MET cc_start: 0.7422 (pp-130) cc_final: 0.7140 (pp-130) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 1.3183 time to fit residues: 80.6121 Evaluate side-chains 50 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 910 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 539 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.111505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.073117 restraints weight = 51767.615| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 4.01 r_work: 0.3056 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12349 Z= 0.156 Angle : 0.576 12.013 16741 Z= 0.297 Chirality : 0.046 0.226 1898 Planarity : 0.004 0.063 2165 Dihedral : 4.717 47.886 1663 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.96 % Allowed : 11.64 % 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: -0.42 (0.21), residues: 1532 helix: 0.51 (0.49), residues: 116 sheet: -0.01 (0.19), residues: 687 loop : -0.57 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 561 HIS 0.004 0.001 HIS B 445 PHE 0.017 0.002 PHE A 998 TYR 0.012 0.001 TYR A 193 ARG 0.007 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 447) hydrogen bonds : angle 5.41371 ( 1254) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.63918 ( 2) covalent geometry : bond 0.00354 (12348) covalent geometry : angle 0.57565 (16739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11500.90 seconds wall clock time: 204 minutes 34.93 seconds (12274.93 seconds total)