Starting phenix.real_space_refine on Wed Mar 4 08:28:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ajm_15484/03_2026/8ajm_15484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ajm_15484/03_2026/8ajm_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_15484/03_2026/8ajm_15484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ajm_15484/03_2026/8ajm_15484.map" model { file = "/net/cci-nas-00/data/ceres_data/8ajm_15484/03_2026/8ajm_15484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ajm_15484/03_2026/8ajm_15484.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.89, per 1000 atoms: 0.24 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: 0.91 Conformation dependent library (CDL) restraints added in 578.8 milliseconds 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: 0.54 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: 3.20 Time building geometry restraints manager: 1.25 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: 2.060 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG A 388 TYR 0.035 0.004 TYR A 239 PHE 0.052 0.005 PHE A 998 TRP 0.053 0.006 TRP B 308 HIS 0.010 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00813 (12348) covalent geometry : angle 0.82498 (16739) SS BOND : bond 0.00357 ( 1) SS BOND : angle 2.21030 ( 2) hydrogen bonds : bond 0.17700 ( 447) hydrogen bonds : angle 8.47811 ( 1254) *********************** 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 : 0.449 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: 0.8097 time to fit residues: 125.7577 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 : 0.461 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN B 110 ASN B 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.113344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.076734 restraints weight = 36850.592| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.41 r_work: 0.3168 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12349 Z= 0.145 Angle : 0.590 8.589 16741 Z= 0.318 Chirality : 0.047 0.152 1898 Planarity : 0.004 0.042 2165 Dihedral : 5.224 37.523 1666 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.85 % Allowed : 6.82 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1532 helix: -0.11 (0.49), residues: 113 sheet: 0.47 (0.19), residues: 682 loop : -0.10 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 101 TYR 0.015 0.002 TYR A 193 PHE 0.018 0.002 PHE A 998 TRP 0.025 0.002 TRP A 561 HIS 0.005 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00319 (12348) covalent geometry : angle 0.58939 (16739) SS BOND : bond 0.00231 ( 1) SS BOND : angle 1.31889 ( 2) hydrogen bonds : bond 0.04220 ( 447) hydrogen bonds : angle 6.04238 ( 1254) *********************** 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 96 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.427 Fit side-chains REVERT: A 178 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7685 (tp) REVERT: A 350 MET cc_start: 0.8800 (mtp) cc_final: 0.8457 (mtm) REVERT: A 782 PHE cc_start: 0.8088 (t80) cc_final: 0.7668 (t80) REVERT: A 896 GLU cc_start: 0.8855 (mp0) cc_final: 0.8621 (pm20) REVERT: A 1062 ILE cc_start: 0.8646 (tt) cc_final: 0.8293 (pp) REVERT: B 109 CYS cc_start: 0.8306 (t) cc_final: 0.7952 (t) outliers start: 25 outliers final: 4 residues processed: 90 average time/residue: 0.7536 time to fit residues: 72.4937 Evaluate side-chains 56 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 207 MET 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 85 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 42 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 A 790 ASN A 950 ASN B 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.109119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071074 restraints weight = 35335.909| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.44 r_work: 0.3050 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 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 = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 12349 Z= 0.379 Angle : 0.719 7.293 16741 Z= 0.380 Chirality : 0.050 0.168 1898 Planarity : 0.005 0.044 2165 Dihedral : 5.599 32.665 1665 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.59 % Allowed : 7.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1532 helix: 0.15 (0.49), residues: 111 sheet: 0.13 (0.19), residues: 686 loop : -0.48 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 101 TYR 0.018 0.002 TYR A 193 PHE 0.031 0.003 PHE A 998 TRP 0.028 0.002 TRP A 561 HIS 0.005 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00861 (12348) covalent geometry : angle 0.71860 (16739) SS BOND : bond 0.00338 ( 1) SS BOND : angle 1.28739 ( 2) hydrogen bonds : bond 0.04406 ( 447) hydrogen bonds : angle 6.23380 ( 1254) *********************** 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 92 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 0.435 Fit side-chains REVERT: A 178 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7735 (mm) REVERT: A 350 MET cc_start: 0.8731 (mtp) cc_final: 0.8483 (mtp) REVERT: A 782 PHE cc_start: 0.8191 (t80) cc_final: 0.7649 (t80) REVERT: A 990 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8467 (mp10) REVERT: A 1054 MET cc_start: 0.8478 (ttp) cc_final: 0.8114 (mtp) REVERT: A 1062 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8326 (pp) REVERT: B 109 CYS cc_start: 0.8503 (t) cc_final: 0.8168 (t) outliers start: 35 outliers final: 13 residues processed: 84 average time/residue: 0.6585 time to fit residues: 59.9599 Evaluate side-chains 65 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 299 ASP 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 22 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 0.0970 chunk 44 optimal weight: 30.0000 chunk 144 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.112520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.073866 restraints weight = 66154.330| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.44 r_work: 0.3071 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12349 Z= 0.111 Angle : 0.546 9.216 16741 Z= 0.292 Chirality : 0.045 0.150 1898 Planarity : 0.004 0.045 2165 Dihedral : 4.866 32.170 1663 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.26 % Allowed : 9.12 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1532 helix: 0.17 (0.49), residues: 116 sheet: 0.17 (0.19), residues: 681 loop : -0.44 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 114 TYR 0.014 0.001 TYR A 42 PHE 0.013 0.001 PHE A1030 TRP 0.021 0.001 TRP A 561 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00238 (12348) covalent geometry : angle 0.54604 (16739) SS BOND : bond 0.00241 ( 1) SS BOND : angle 0.96342 ( 2) hydrogen bonds : bond 0.03284 ( 447) hydrogen bonds : angle 5.55556 ( 1254) *********************** 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 69 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.420 Fit side-chains REVERT: A 178 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 782 PHE cc_start: 0.8095 (t80) cc_final: 0.7748 (t80) REVERT: A 896 GLU cc_start: 0.8920 (mp0) cc_final: 0.8709 (pm20) REVERT: A 1062 ILE cc_start: 0.8673 (tt) cc_final: 0.8347 (pp) REVERT: B 109 CYS cc_start: 0.8453 (t) cc_final: 0.8105 (t) outliers start: 17 outliers final: 8 residues processed: 66 average time/residue: 0.6827 time to fit residues: 48.7158 Evaluate side-chains 58 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 768 SER 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 B residue 334 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 32 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.112046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073148 restraints weight = 54342.403| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.14 r_work: 0.3081 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 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 = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12349 Z= 0.137 Angle : 0.537 9.347 16741 Z= 0.284 Chirality : 0.045 0.154 1898 Planarity : 0.004 0.051 2165 Dihedral : 4.694 36.957 1663 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.26 % Allowed : 9.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1532 helix: 0.39 (0.49), residues: 116 sheet: 0.14 (0.19), residues: 692 loop : -0.40 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 114 TYR 0.012 0.001 TYR A 193 PHE 0.018 0.002 PHE A 998 TRP 0.020 0.001 TRP A 561 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00308 (12348) covalent geometry : angle 0.53705 (16739) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.76304 ( 2) hydrogen bonds : bond 0.03193 ( 447) hydrogen bonds : angle 5.42448 ( 1254) *********************** 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 70 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.548 Fit side-chains REVERT: A 178 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7744 (mm) REVERT: A 350 MET cc_start: 0.8743 (mtp) cc_final: 0.8482 (mtm) REVERT: A 782 PHE cc_start: 0.8086 (t80) cc_final: 0.7746 (t80) REVERT: A 1062 ILE cc_start: 0.8624 (tt) cc_final: 0.8375 (pp) outliers start: 17 outliers final: 8 residues processed: 66 average time/residue: 0.6548 time to fit residues: 46.9842 Evaluate side-chains 55 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 768 SER Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 207 MET 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 93 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 40.0000 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.110669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.073134 restraints weight = 35203.931| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.36 r_work: 0.3079 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 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 = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12349 Z= 0.210 Angle : 0.578 9.996 16741 Z= 0.305 Chirality : 0.046 0.153 1898 Planarity : 0.004 0.059 2165 Dihedral : 4.904 44.002 1663 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.78 % Allowed : 10.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1532 helix: 0.53 (0.50), residues: 114 sheet: 0.02 (0.19), residues: 685 loop : -0.55 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 114 TYR 0.013 0.001 TYR A 5 PHE 0.023 0.002 PHE A 998 TRP 0.017 0.001 TRP A 561 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00477 (12348) covalent geometry : angle 0.57840 (16739) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.72413 ( 2) hydrogen bonds : bond 0.03385 ( 447) hydrogen bonds : angle 5.61376 ( 1254) *********************** 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 75 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.378 Fit side-chains REVERT: A 178 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7719 (mm) REVERT: A 350 MET cc_start: 0.8699 (mtp) cc_final: 0.8453 (mtm) REVERT: A 782 PHE cc_start: 0.8159 (t80) cc_final: 0.7834 (t80) REVERT: A 1062 ILE cc_start: 0.8592 (tt) cc_final: 0.8390 (pp) outliers start: 24 outliers final: 11 residues processed: 69 average time/residue: 0.6009 time to fit residues: 45.4097 Evaluate side-chains 59 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 1109 VAL Chi-restraints excluded: chain B residue 57 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 13 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 40.0000 chunk 150 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.111246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072663 restraints weight = 60268.771| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.24 r_work: 0.3040 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 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 = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12349 Z= 0.163 Angle : 0.555 10.686 16741 Z= 0.291 Chirality : 0.045 0.155 1898 Planarity : 0.004 0.058 2165 Dihedral : 4.774 46.275 1663 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.63 % Allowed : 10.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.20), residues: 1532 helix: 0.53 (0.49), residues: 116 sheet: 0.05 (0.19), residues: 676 loop : -0.59 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 114 TYR 0.012 0.001 TYR A 5 PHE 0.018 0.002 PHE A 998 TRP 0.029 0.002 TRP A 561 HIS 0.006 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00370 (12348) covalent geometry : angle 0.55509 (16739) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.75349 ( 2) hydrogen bonds : bond 0.03153 ( 447) hydrogen bonds : angle 5.44838 ( 1254) *********************** 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 70 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.406 Fit side-chains REVERT: A 178 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 350 MET cc_start: 0.8735 (mtp) cc_final: 0.8475 (mtm) REVERT: A 782 PHE cc_start: 0.8108 (t80) cc_final: 0.7713 (t80) outliers start: 22 outliers final: 11 residues processed: 65 average time/residue: 0.6512 time to fit residues: 46.2007 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 : 0.449 ------------------------------------------------------------------------------- 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 768 SER Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain B residue 57 LEU 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 96 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 50.0000 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.110211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072296 restraints weight = 69340.676| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.40 r_work: 0.3009 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3565 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= 0.213 Angle : 0.590 11.316 16741 Z= 0.308 Chirality : 0.046 0.158 1898 Planarity : 0.004 0.064 2165 Dihedral : 4.906 48.201 1663 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.15 % Allowed : 10.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1532 helix: 0.49 (0.49), residues: 116 sheet: -0.06 (0.19), residues: 676 loop : -0.64 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 114 TYR 0.012 0.001 TYR A 5 PHE 0.023 0.002 PHE A 998 TRP 0.024 0.002 TRP A 561 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00486 (12348) covalent geometry : angle 0.59035 (16739) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.63954 ( 2) hydrogen bonds : bond 0.03292 ( 447) hydrogen bonds : angle 5.59170 ( 1254) *********************** 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 78 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 49 time to evaluate : 0.303 Fit side-chains REVERT: A 178 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7744 (mm) REVERT: A 350 MET cc_start: 0.8748 (mtp) cc_final: 0.8534 (mtm) REVERT: A 782 PHE cc_start: 0.8140 (t80) cc_final: 0.7786 (t80) outliers start: 29 outliers final: 15 residues processed: 73 average time/residue: 0.5956 time to fit residues: 47.7318 Evaluate side-chains 60 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 768 SER Chi-restraints excluded: chain A residue 1109 VAL 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 235 ILE 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 88 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 40.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.110667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.072002 restraints weight = 49276.735| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.94 r_work: 0.3043 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 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 = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12349 Z= 0.184 Angle : 0.578 11.821 16741 Z= 0.302 Chirality : 0.046 0.157 1898 Planarity : 0.004 0.062 2165 Dihedral : 4.873 48.227 1663 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.78 % Allowed : 10.53 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1532 helix: 0.43 (0.49), residues: 116 sheet: -0.08 (0.19), residues: 683 loop : -0.61 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 753 TYR 0.012 0.001 TYR A 5 PHE 0.022 0.002 PHE A 998 TRP 0.024 0.002 TRP A 561 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00417 (12348) covalent geometry : angle 0.57756 (16739) SS BOND : bond 0.00276 ( 1) SS BOND : angle 0.64952 ( 2) hydrogen bonds : bond 0.03265 ( 447) hydrogen bonds : angle 5.53383 ( 1254) *********************** 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 70 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.459 Fit side-chains REVERT: A 178 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7791 (mm) REVERT: A 350 MET cc_start: 0.8709 (mtp) cc_final: 0.8464 (mtm) REVERT: A 782 PHE cc_start: 0.8141 (t80) cc_final: 0.7691 (t80) REVERT: A 910 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8309 (tmm) outliers start: 24 outliers final: 13 residues processed: 65 average time/residue: 0.6777 time to fit residues: 47.9957 Evaluate side-chains 57 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 B residue 425 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.109995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.071301 restraints weight = 49556.727| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.92 r_work: 0.3027 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 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 = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12349 Z= 0.236 Angle : 0.610 9.158 16741 Z= 0.320 Chirality : 0.046 0.151 1898 Planarity : 0.004 0.064 2165 Dihedral : 5.021 49.159 1663 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.33 % Allowed : 11.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1532 helix: 0.29 (0.48), residues: 120 sheet: -0.16 (0.19), residues: 677 loop : -0.77 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 753 TYR 0.012 0.001 TYR A 5 PHE 0.025 0.002 PHE A 998 TRP 0.022 0.002 TRP A 561 HIS 0.005 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00538 (12348) covalent geometry : angle 0.60955 (16739) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.62804 ( 2) hydrogen bonds : bond 0.03379 ( 447) hydrogen bonds : angle 5.69233 ( 1254) ********************** 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 65 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.481 Fit side-chains REVERT: A 178 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7757 (mm) REVERT: A 350 MET cc_start: 0.8713 (mtp) cc_final: 0.8477 (mtm) REVERT: A 782 PHE cc_start: 0.8181 (t80) cc_final: 0.7823 (t80) REVERT: A 910 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8315 (tmm) outliers start: 18 outliers final: 11 residues processed: 63 average time/residue: 0.6191 time to fit residues: 42.6832 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 : 0.427 ------------------------------------------------------------------------------- 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 768 SER Chi-restraints excluded: chain A residue 910 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.111227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.072607 restraints weight = 49098.117| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.92 r_work: 0.3064 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 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 = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1572 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12349 Z= 0.154 Angle : 0.580 9.248 16741 Z= 0.302 Chirality : 0.045 0.153 1898 Planarity : 0.004 0.064 2165 Dihedral : 4.842 48.726 1663 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.26 % Allowed : 11.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1532 helix: 0.40 (0.48), residues: 122 sheet: -0.12 (0.19), residues: 685 loop : -0.69 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 753 TYR 0.017 0.001 TYR A 518 PHE 0.019 0.002 PHE A 998 TRP 0.020 0.001 TRP A 561 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00350 (12348) covalent geometry : angle 0.58026 (16739) SS BOND : bond 0.00272 ( 1) SS BOND : angle 0.68224 ( 2) hydrogen bonds : bond 0.03121 ( 447) hydrogen bonds : angle 5.48517 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4701.99 seconds wall clock time: 80 minutes 32.38 seconds (4832.38 seconds total)