Starting phenix.real_space_refine on Thu Jul 2 19:42:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxg_36700/07_2026/8jxg_36700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxg_36700/07_2026/8jxg_36700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxg_36700/07_2026/8jxg_36700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxg_36700/07_2026/8jxg_36700.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxg_36700/07_2026/8jxg_36700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxg_36700/07_2026/8jxg_36700.cif" } resolution = 3.2 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 137 5.16 5 C 5903 2.51 5 N 1721 2.21 5 O 2028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9810 Number of models: 1 Model: "" Number of chains: 11 Chain: "D" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 599 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "A" Number of atoms: 8739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8739 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 55, 'TRANS': 1058} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 84 Ad-hoc single atom residues: {' CA': 21} Unusual residues: {'A2G': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 21 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.30, per 1000 atoms: 0.23 Number of scatterers: 9810 At special positions: 0 Unit cell: (95.948, 128.401, 145.333, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 137 16.00 O 2028 8.00 N 1721 7.00 C 5903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=61, symmetry=0 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1238 " - pdb=" SG CYS A1257 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1267 " distance=2.03 Simple disulfide: pdb=" SG CYS A2865 " - pdb=" SG CYS A2878 " distance=2.03 Simple disulfide: pdb=" SG CYS A2872 " - pdb=" SG CYS A2891 " distance=2.03 Simple disulfide: pdb=" SG CYS A2885 " - pdb=" SG CYS A2901 " distance=2.03 Simple disulfide: pdb=" SG CYS A2908 " - pdb=" SG CYS A2920 " distance=2.03 Simple disulfide: pdb=" SG CYS A2915 " - pdb=" SG CYS A2933 " distance=2.03 Simple disulfide: pdb=" SG CYS A2927 " - pdb=" SG CYS A2945 " distance=2.03 Simple disulfide: pdb=" SG CYS A2950 " - pdb=" SG CYS A2967 " distance=2.03 Simple disulfide: pdb=" SG CYS A2957 " - pdb=" SG CYS A2980 " distance=2.03 Simple disulfide: pdb=" SG CYS A2974 " - pdb=" SG CYS A2990 " distance=2.03 Simple disulfide: pdb=" SG CYS A2995 " - pdb=" SG CYS A3007 " distance=2.03 Simple disulfide: pdb=" SG CYS A3002 " - pdb=" SG CYS A3020 " distance=2.03 Simple disulfide: pdb=" SG CYS A3014 " - pdb=" SG CYS A3029 " distance=2.03 Simple disulfide: pdb=" SG CYS A3034 " - pdb=" SG CYS A3046 " distance=2.03 Simple disulfide: pdb=" SG CYS A3041 " - pdb=" SG CYS A3059 " distance=2.03 Simple disulfide: pdb=" SG CYS A3053 " - pdb=" SG CYS A3070 " distance=2.03 Simple disulfide: pdb=" SG CYS A3077 " - pdb=" SG CYS A3089 " distance=2.03 Simple disulfide: pdb=" SG CYS A3084 " - pdb=" SG CYS A3102 " distance=2.03 Simple disulfide: pdb=" SG CYS A3096 " - pdb=" SG CYS A3111 " distance=2.04 Simple disulfide: pdb=" SG CYS A3116 " - pdb=" SG CYS A3128 " distance=2.03 Simple disulfide: pdb=" SG CYS A3124 " - pdb=" SG CYS A3137 " distance=2.03 Simple disulfide: pdb=" SG CYS A3139 " - pdb=" SG CYS A3152 " distance=2.03 Simple disulfide: pdb=" SG CYS A3158 " - pdb=" SG CYS A3169 " distance=2.03 Simple disulfide: pdb=" SG CYS A3165 " - pdb=" SG CYS A3178 " distance=2.03 Simple disulfide: pdb=" SG CYS A3180 " - pdb=" SG CYS A3193 " distance=2.03 Simple disulfide: pdb=" SG CYS A3313 " - pdb=" SG CYS A3321 " distance=2.03 Simple disulfide: pdb=" SG CYS A3471 " - pdb=" SG CYS A3482 " distance=2.03 Simple disulfide: pdb=" SG CYS A3478 " - pdb=" SG CYS A3493 " distance=2.03 Simple disulfide: pdb=" SG CYS A3495 " - pdb=" SG CYS A3510 " distance=2.03 Simple disulfide: pdb=" SG CYS A3514 " - pdb=" SG CYS A3527 " distance=2.03 Simple disulfide: pdb=" SG CYS A3521 " - pdb=" SG CYS A3540 " distance=2.03 Simple disulfide: pdb=" SG CYS A3534 " - pdb=" SG CYS A3550 " distance=2.03 Simple disulfide: pdb=" SG CYS A3555 " - pdb=" SG CYS A3567 " distance=2.03 Simple disulfide: pdb=" SG CYS A3562 " - pdb=" SG CYS A3580 " distance=2.03 Simple disulfide: pdb=" SG CYS A3574 " - pdb=" SG CYS A3591 " distance=2.03 Simple disulfide: pdb=" SG CYS A3596 " - pdb=" SG CYS A3608 " distance=2.03 Simple disulfide: pdb=" SG CYS A3603 " - pdb=" SG CYS A3621 " distance=2.03 Simple disulfide: pdb=" SG CYS A3615 " - pdb=" SG CYS A3632 " distance=2.03 Simple disulfide: pdb=" SG CYS A3637 " - pdb=" SG CYS A3649 " distance=2.03 Simple disulfide: pdb=" SG CYS A3644 " - pdb=" SG CYS A3662 " distance=2.03 Simple disulfide: pdb=" SG CYS A3656 " - pdb=" SG CYS A3673 " distance=2.03 Simple disulfide: pdb=" SG CYS A3680 " - pdb=" SG CYS A3694 " distance=2.03 Simple disulfide: pdb=" SG CYS A3688 " - pdb=" SG CYS A3707 " distance=2.03 Simple disulfide: pdb=" SG CYS A3701 " - pdb=" SG CYS A3716 " distance=2.03 Simple disulfide: pdb=" SG CYS A3721 " - pdb=" SG CYS A3734 " distance=2.03 Simple disulfide: pdb=" SG CYS A3729 " - pdb=" SG CYS A3747 " distance=2.03 Simple disulfide: pdb=" SG CYS A3741 " - pdb=" SG CYS A3756 " distance=2.03 Simple disulfide: pdb=" SG CYS A3761 " - pdb=" SG CYS A3773 " distance=2.03 Simple disulfide: pdb=" SG CYS A3768 " - pdb=" SG CYS A3786 " distance=2.03 Simple disulfide: pdb=" SG CYS A3780 " - pdb=" SG CYS A3795 " distance=2.03 Simple disulfide: pdb=" SG CYS A3800 " - pdb=" SG CYS A3812 " distance=2.04 Simple disulfide: pdb=" SG CYS A3807 " - pdb=" SG CYS A3825 " distance=2.03 Simple disulfide: pdb=" SG CYS A3819 " - pdb=" SG CYS A3834 " distance=2.03 Simple disulfide: pdb=" SG CYS A3844 " - pdb=" SG CYS A3856 " distance=2.03 Simple disulfide: pdb=" SG CYS A3851 " - pdb=" SG CYS A3869 " distance=2.03 Simple disulfide: pdb=" SG CYS A3863 " - pdb=" SG CYS A3880 " distance=2.03 Simple disulfide: pdb=" SG CYS A3885 " - pdb=" SG CYS A3898 " distance=2.03 Simple disulfide: pdb=" SG CYS A3893 " - pdb=" SG CYS A3911 " distance=2.03 Simple disulfide: pdb=" SG CYS A3905 " - pdb=" SG CYS A3922 " 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=4, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A4701 " - " ASN A3448 " " NAG A4702 " - " ASN A3682 " " NAG B 1 " - " ASN A3127 " " NAG C 1 " - " ASN A3213 " " NAG E 1 " - " ASN A3259 " " NAG F 1 " - " ASN A3317 " " NAG G 1 " - " ASN A3357 " " NAG H 1 " - " ASN A3566 " " NAG I 1 " - " ASN A3840 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 354.4 milliseconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 28 sheets defined 17.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'D' and resid 59 through 72 Processing helix chain 'D' and resid 75 through 102 Processing helix chain 'D' and resid 108 through 125 removed outlier: 4.419A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1250 No H-bonds generated for 'chain 'A' and resid 1248 through 1250' Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.925A pdb=" N HIS A1264 " --> pdb=" O SER A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2923 through 2927 Processing helix chain 'A' and resid 2936 through 2940 Processing helix chain 'A' and resid 2971 through 2973 No H-bonds generated for 'chain 'A' and resid 2971 through 2973' Processing helix chain 'A' and resid 3009 through 3013 Processing helix chain 'A' and resid 3050 through 3052 No H-bonds generated for 'chain 'A' and resid 3050 through 3052' Processing helix chain 'A' and resid 3091 through 3095 removed outlier: 3.557A pdb=" N VAL A3095 " --> pdb=" O MET A3092 " (cutoff:3.500A) Processing helix chain 'A' and resid 3156 through 3161 Processing helix chain 'A' and resid 3162 through 3165 removed outlier: 3.523A pdb=" N CYS A3165 " --> pdb=" O PRO A3162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3162 through 3165' Processing helix chain 'A' and resid 3460 through 3464 Processing helix chain 'A' and resid 3474 through 3478 Processing helix chain 'A' and resid 3531 through 3533 No H-bonds generated for 'chain 'A' and resid 3531 through 3533' Processing helix chain 'A' and resid 3569 through 3573 Processing helix chain 'A' and resid 3583 through 3586 Processing helix chain 'A' and resid 3587 through 3592 Processing helix chain 'A' and resid 3630 through 3635 Processing helix chain 'A' and resid 3653 through 3655 No H-bonds generated for 'chain 'A' and resid 3653 through 3655' Processing helix chain 'A' and resid 3669 through 3674 Processing helix chain 'A' and resid 3675 through 3679 removed outlier: 3.510A pdb=" N TYR A3678 " --> pdb=" O THR A3675 " (cutoff:3.500A) Processing helix chain 'A' and resid 3698 through 3700 No H-bonds generated for 'chain 'A' and resid 3698 through 3700' Processing helix chain 'A' and resid 3710 through 3714 removed outlier: 3.518A pdb=" N GLU A3713 " --> pdb=" O ASN A3710 " (cutoff:3.500A) Processing helix chain 'A' and resid 3715 through 3719 Processing helix chain 'A' and resid 3738 through 3740 No H-bonds generated for 'chain 'A' and resid 3738 through 3740' Processing helix chain 'A' and resid 3777 through 3779 No H-bonds generated for 'chain 'A' and resid 3777 through 3779' Processing helix chain 'A' and resid 3789 through 3793 Processing helix chain 'A' and resid 3816 through 3818 No H-bonds generated for 'chain 'A' and resid 3816 through 3818' Processing helix chain 'A' and resid 3858 through 3862 Processing helix chain 'A' and resid 3872 through 3875 Processing helix chain 'A' and resid 3876 through 3882 removed outlier: 4.094A pdb=" N ASN A3882 " --> pdb=" O HIS A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3904 No H-bonds generated for 'chain 'A' and resid 3902 through 3904' Processing helix chain 'A' and resid 3914 through 3922 removed outlier: 6.658A pdb=" N GLU A3919 " --> pdb=" O ASP A3916 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU A3920 " --> pdb=" O GLU A3917 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS A3921 " --> pdb=" O LYS A3918 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A3922 " --> pdb=" O GLU A3919 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1235 through 1237 Processing sheet with id=AA2, first strand: chain 'A' and resid 2869 through 2871 Processing sheet with id=AA3, first strand: chain 'A' and resid 2913 through 2914 Processing sheet with id=AA4, first strand: chain 'A' and resid 2954 through 2956 Processing sheet with id=AA5, first strand: chain 'A' and resid 3000 through 3001 Processing sheet with id=AA6, first strand: chain 'A' and resid 3038 through 3040 Processing sheet with id=AA7, first strand: chain 'A' and resid 3127 through 3130 Processing sheet with id=AA8, first strand: chain 'A' and resid 3143 through 3145 Processing sheet with id=AA9, first strand: chain 'A' and resid 3168 through 3171 Processing sheet with id=AB1, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id=AB2, first strand: chain 'A' and resid 3221 through 3225 removed outlier: 6.527A pdb=" N ILE A3211 " --> pdb=" O ILE A3224 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A3202 " --> pdb=" O TYR A3459 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER A3206 " --> pdb=" O ASP A3455 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP A3455 " --> pdb=" O SER A3206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3235 through 3237 removed outlier: 6.748A pdb=" N ARG A3255 " --> pdb=" O THR A3265 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR A3265 " --> pdb=" O ARG A3255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3274 through 3280 removed outlier: 4.128A pdb=" N SER A3276 " --> pdb=" O LEU A3289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP A3288 " --> pdb=" O PHE A3297 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A3296 " --> pdb=" O ILE A3309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3325 through 3331 removed outlier: 4.285A pdb=" N ILE A3328 " --> pdb=" O TYR A3338 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR A3338 " --> pdb=" O ILE A3328 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A3330 " --> pdb=" O HIS A3336 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N HIS A3336 " --> pdb=" O LEU A3330 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP A3339 " --> pdb=" O GLY A3349 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A3348 " --> pdb=" O ILE A3361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3371 through 3374 removed outlier: 3.777A pdb=" N ALA A3371 " --> pdb=" O ALA A3384 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A3391 " --> pdb=" O VAL A3404 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3412 through 3418 removed outlier: 3.965A pdb=" N ALA A3414 " --> pdb=" O THR A3425 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A3432 " --> pdb=" O LEU A3446 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3481 through 3484 Processing sheet with id=AB9, first strand: chain 'A' and resid 3499 through 3503 Processing sheet with id=AC1, first strand: chain 'A' and resid 3518 through 3520 Processing sheet with id=AC2, first strand: chain 'A' and resid 3560 through 3561 Processing sheet with id=AC3, first strand: chain 'A' and resid 3600 through 3602 Processing sheet with id=AC4, first strand: chain 'A' and resid 3641 through 3643 Processing sheet with id=AC5, first strand: chain 'A' and resid 3685 through 3687 Processing sheet with id=AC6, first strand: chain 'A' and resid 3726 through 3728 Processing sheet with id=AC7, first strand: chain 'A' and resid 3765 through 3767 Processing sheet with id=AC8, first strand: chain 'A' and resid 3804 through 3806 Processing sheet with id=AC9, first strand: chain 'A' and resid 3849 through 3850 Processing sheet with id=AD1, first strand: chain 'A' and resid 3890 through 3893 203 hydrogen bonds defined for protein. 468 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: 2.28 Time building geometry restraints manager: 1.52 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: 2833 1.33 - 1.46: 2134 1.46 - 1.58: 4890 1.58 - 1.70: 1 1.70 - 1.83: 151 Bond restraints: 10009 Sorted by residual: bond pdb=" N MET A2936 " pdb=" CA MET A2936 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.16e+00 bond pdb=" N THR A3799 " pdb=" CA THR A3799 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.22e-02 6.72e+03 7.90e+00 bond pdb=" N THR A3836 " pdb=" CA THR A3836 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.30e-02 5.92e+03 7.22e+00 bond pdb=" N CYS A3800 " pdb=" CA CYS A3800 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.23e-02 6.61e+03 6.98e+00 bond pdb=" N MET A3848 " pdb=" CA MET A3848 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.42e+00 ... (remaining 10004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12916 1.75 - 3.50: 512 3.50 - 5.25: 106 5.25 - 7.00: 23 7.00 - 8.76: 2 Bond angle restraints: 13559 Sorted by residual: angle pdb=" C HIS A3312 " pdb=" CA HIS A3312 " pdb=" CB HIS A3312 " ideal model delta sigma weight residual 117.23 110.60 6.63 1.36e+00 5.41e-01 2.37e+01 angle pdb=" N PRO A3845 " pdb=" CA PRO A3845 " pdb=" C PRO A3845 " ideal model delta sigma weight residual 111.41 104.83 6.58 1.50e+00 4.44e-01 1.92e+01 angle pdb=" CA ASP A3379 " pdb=" CB ASP A3379 " pdb=" CG ASP A3379 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C GLY A3110 " pdb=" N CYS A3111 " pdb=" CA CYS A3111 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" CA MET A3848 " pdb=" C MET A3848 " pdb=" O MET A3848 " ideal model delta sigma weight residual 121.81 118.04 3.77 1.18e+00 7.18e-01 1.02e+01 ... (remaining 13554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.52: 5958 22.52 - 45.04: 476 45.04 - 67.57: 82 67.57 - 90.09: 67 90.09 - 112.61: 28 Dihedral angle restraints: 6611 sinusoidal: 3171 harmonic: 3440 Sorted by residual: dihedral pdb=" CB CYS A3534 " pdb=" SG CYS A3534 " pdb=" SG CYS A3550 " pdb=" CB CYS A3550 " ideal model delta sinusoidal sigma weight residual 93.00 177.00 -84.00 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS A2950 " pdb=" SG CYS A2950 " pdb=" SG CYS A2967 " pdb=" CB CYS A2967 " ideal model delta sinusoidal sigma weight residual 93.00 168.96 -75.96 1 1.00e+01 1.00e-02 7.27e+01 dihedral pdb=" CB CYS A1238 " pdb=" SG CYS A1238 " pdb=" SG CYS A1257 " pdb=" CB CYS A1257 " ideal model delta sinusoidal sigma weight residual 93.00 166.69 -73.69 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 6608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1339 0.084 - 0.168: 136 0.168 - 0.252: 8 0.252 - 0.336: 2 0.336 - 0.420: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" C1 NAG A4701 " pdb=" ND2 ASN A3448 " pdb=" C2 NAG A4701 " pdb=" O5 NAG A4701 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A3566 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1 NAG A4702 " pdb=" ND2 ASN A3682 " pdb=" C2 NAG A4702 " pdb=" O5 NAG A4702 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1483 not shown) Planarity restraints: 1805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A4701 " 0.323 2.00e-02 2.50e+03 2.74e-01 9.37e+02 pdb=" C7 NAG A4701 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A4701 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A4701 " -0.477 2.00e-02 2.50e+03 pdb=" O7 NAG A4701 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.319 2.00e-02 2.50e+03 2.73e-01 9.33e+02 pdb=" C7 NAG F 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.481 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.324 2.00e-02 2.50e+03 2.73e-01 9.32e+02 pdb=" C7 NAG G 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.193 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.471 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.037 2.00e-02 2.50e+03 ... (remaining 1802 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 860 2.74 - 3.28: 10370 3.28 - 3.82: 16087 3.82 - 4.36: 19577 4.36 - 4.90: 32626 Nonbonded interactions: 79520 Sorted by model distance: nonbonded pdb=" OD1 ASP A3657 " pdb="CA CA A4721 " model vdw 2.194 3.250 nonbonded pdb=" N ASP A2938 " pdb=" OD1 ASP A2938 " model vdw 2.200 3.120 nonbonded pdb=" O TRP A3778 " pdb="CA CA A4724 " model vdw 2.203 3.250 nonbonded pdb=" OD1 ASP A3820 " pdb="CA CA A4725 " model vdw 2.203 3.250 nonbonded pdb=" OD1 ASN A3575 " pdb="CA CA A4719 " model vdw 2.210 3.250 ... (remaining 79515 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.930 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.007 0.473 10103 Z= 0.544 Angle : 0.850 10.116 13768 Z= 0.432 Chirality : 0.052 0.420 1486 Planarity : 0.015 0.274 1796 Dihedral : 19.602 112.608 4204 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.03 % Favored : 92.80 % Rotamer: Outliers : 2.17 % Allowed : 15.73 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.24), residues: 1180 helix: -1.23 (0.53), residues: 88 sheet: -0.79 (0.40), residues: 155 loop : -0.42 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3017 TYR 0.011 0.001 TYR A3459 PHE 0.023 0.001 PHE A2884 TRP 0.020 0.001 TRP D 66 HIS 0.007 0.001 HIS A1254 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.25 (10009) covalent geometry : angle 0.82499 / 0.43 (13559) SS BOND : bond 0.00253 / 0.18 ( 61) SS BOND : angle 0.84833 / 0.59 ( 122) hydrogen bonds : bond 0.26383 / 16.50 ( 203) hydrogen bonds : angle 9.66975 / 6.94 ( 468) Misc. bond : bond 0.24207 / 11.56 ( 4) link_ALPHA1-3 : bond 0.01130 / 0.55 ( 3) link_ALPHA1-3 : angle 1.41038 / 0.66 ( 9) link_ALPHA1-6 : bond 0.00731 / 0.36 ( 3) link_ALPHA1-6 : angle 1.00971 / 0.53 ( 9) link_BETA1-4 : bond 0.00747 / 0.51 ( 14) link_BETA1-4 : angle 1.93029 / 1.39 ( 42) link_NAG-ASN : bond 0.00965 / 0.56 ( 9) link_NAG-ASN : angle 4.06253 / 2.37 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 114 LEU cc_start: 0.1135 (OUTLIER) cc_final: 0.0771 (pt) outliers start: 23 outliers final: 21 residues processed: 88 average time/residue: 0.0943 time to fit residues: 12.3141 Evaluate side-chains 80 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 3047 ILE Chi-restraints excluded: chain A residue 3096 CYS Chi-restraints excluded: chain A residue 3106 SER Chi-restraints excluded: chain A residue 3220 SER Chi-restraints excluded: chain A residue 3224 ILE Chi-restraints excluded: chain A residue 3228 LEU Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3449 THR Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3509 LEU Chi-restraints excluded: chain A residue 3549 LEU Chi-restraints excluded: chain A residue 3623 ASP Chi-restraints excluded: chain A residue 3770 ASP Chi-restraints excluded: chain A residue 3836 THR Chi-restraints excluded: chain A residue 3874 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.0050 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0020 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3066 GLN A3262 ASN A3523 ASN A3878 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.154770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109976 restraints weight = 16908.510| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.15 r_work: 0.3384 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10103 Z= 0.146 Angle : 0.734 10.013 13768 Z= 0.361 Chirality : 0.049 0.313 1486 Planarity : 0.005 0.040 1796 Dihedral : 14.220 92.166 1995 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.30 % Allowed : 14.69 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.25), residues: 1180 helix: -0.53 (0.52), residues: 94 sheet: -0.71 (0.39), residues: 174 loop : -0.48 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 78 TYR 0.010 0.001 TYR A3459 PHE 0.018 0.002 PHE A2884 TRP 0.019 0.001 TRP D 66 HIS 0.008 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (10009) covalent geometry : angle 0.69391 / 0.35 (13559) SS BOND : bond 0.00382 / 0.29 ( 61) SS BOND : angle 0.82794 / 0.61 ( 122) hydrogen bonds : bond 0.05598 / 3.63 ( 203) hydrogen bonds : angle 6.67082 / 4.69 ( 468) Misc. bond : bond 0.00711 / 0.34 ( 4) link_ALPHA1-3 : bond 0.01738 / 0.85 ( 3) link_ALPHA1-3 : angle 1.82302 / 1.00 ( 9) link_ALPHA1-6 : bond 0.01195 / 0.59 ( 3) link_ALPHA1-6 : angle 1.73339 / 0.89 ( 9) link_BETA1-4 : bond 0.00757 / 0.52 ( 14) link_BETA1-4 : angle 2.53404 / 1.71 ( 42) link_NAG-ASN : bond 0.00874 / 0.48 ( 9) link_NAG-ASN : angle 4.17810 / 2.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5539 (mttt) cc_final: 0.5080 (mmtm) REVERT: A 1230 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8166 (ttm) REVERT: A 2919 ARG cc_start: 0.2602 (OUTLIER) cc_final: 0.1711 (mtp85) REVERT: A 2992 MET cc_start: 0.4983 (mmm) cc_final: 0.4780 (mmm) REVERT: A 3150 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6774 (ttt-90) REVERT: A 3275 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7809 (mm-30) outliers start: 35 outliers final: 21 residues processed: 95 average time/residue: 0.0930 time to fit residues: 13.0283 Evaluate side-chains 83 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain A residue 1230 MET Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2927 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 3096 CYS Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3228 LEU Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3513 MET Chi-restraints excluded: chain A residue 3549 LEU Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3680 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3874 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3336 HIS A3801 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.153254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107382 restraints weight = 17178.744| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.22 r_work: 0.3342 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10103 Z= 0.177 Angle : 0.710 9.373 13768 Z= 0.349 Chirality : 0.051 0.304 1486 Planarity : 0.004 0.040 1796 Dihedral : 12.102 80.021 1975 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.67 % Allowed : 14.50 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.25), residues: 1180 helix: -0.43 (0.53), residues: 95 sheet: -0.93 (0.41), residues: 164 loop : -0.50 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3923 TYR 0.014 0.002 TYR D 125 PHE 0.019 0.002 PHE A2884 TRP 0.014 0.002 TRP D 66 HIS 0.005 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (10009) covalent geometry : angle 0.67455 / 0.34 (13559) SS BOND : bond 0.00269 / 0.16 ( 61) SS BOND : angle 0.85686 / 0.58 ( 122) hydrogen bonds : bond 0.05095 / 3.30 ( 203) hydrogen bonds : angle 6.32779 / 4.42 ( 468) Misc. bond : bond 0.00081 / 0.04 ( 4) link_ALPHA1-3 : bond 0.01941 / 0.95 ( 3) link_ALPHA1-3 : angle 1.79443 / 0.94 ( 9) link_ALPHA1-6 : bond 0.01342 / 0.67 ( 3) link_ALPHA1-6 : angle 1.53193 / 0.78 ( 9) link_BETA1-4 : bond 0.00707 / 0.45 ( 14) link_BETA1-4 : angle 2.53049 / 1.75 ( 42) link_NAG-ASN : bond 0.00648 / 0.34 ( 9) link_NAG-ASN : angle 3.70730 / 2.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5487 (mttt) cc_final: 0.5171 (mmtm) REVERT: A 1230 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8271 (ttm) REVERT: A 2919 ARG cc_start: 0.2648 (OUTLIER) cc_final: 0.1769 (mtp85) REVERT: A 2938 ASP cc_start: 0.0729 (OUTLIER) cc_final: 0.0288 (p0) REVERT: A 2961 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6349 (mmt180) REVERT: A 3092 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5677 (pmt) REVERT: A 3146 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6705 (pmm) REVERT: A 3275 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 3664 ASP cc_start: 0.8600 (t0) cc_final: 0.8265 (t0) REVERT: A 3680 CYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7631 (m) REVERT: A 3807 CYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7531 (m) outliers start: 39 outliers final: 23 residues processed: 90 average time/residue: 0.1017 time to fit residues: 13.1173 Evaluate side-chains 88 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain A residue 1230 MET Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2927 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 2961 ARG Chi-restraints excluded: chain A residue 2993 ARG Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3096 CYS Chi-restraints excluded: chain A residue 3146 MET Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3228 LEU Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3353 MET Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3513 MET Chi-restraints excluded: chain A residue 3549 LEU Chi-restraints excluded: chain A residue 3578 GLN Chi-restraints excluded: chain A residue 3680 CYS Chi-restraints excluded: chain A residue 3695 ILE Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3807 CYS Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3874 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 13 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 0.0000 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 0.0270 chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 91 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 0.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2959 ASN A3378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.156501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111603 restraints weight = 17166.909| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.24 r_work: 0.3404 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10103 Z= 0.115 Angle : 0.634 8.907 13768 Z= 0.311 Chirality : 0.048 0.292 1486 Planarity : 0.004 0.040 1796 Dihedral : 9.921 69.339 1975 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.24 % Allowed : 14.41 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.25), residues: 1180 helix: -0.47 (0.53), residues: 94 sheet: -0.73 (0.40), residues: 174 loop : -0.40 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3822 TYR 0.010 0.001 TYR D 125 PHE 0.018 0.002 PHE A2884 TRP 0.012 0.001 TRP A3383 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (10009) covalent geometry : angle 0.60101 / 0.30 (13559) SS BOND : bond 0.00210 / 0.12 ( 61) SS BOND : angle 0.88148 / 0.60 ( 122) hydrogen bonds : bond 0.04159 / 2.71 ( 203) hydrogen bonds : angle 5.85205 / 4.07 ( 468) Misc. bond : bond 0.00056 / 0.03 ( 4) link_ALPHA1-3 : bond 0.01567 / 0.77 ( 3) link_ALPHA1-3 : angle 1.60106 / 0.84 ( 9) link_ALPHA1-6 : bond 0.01704 / 0.84 ( 3) link_ALPHA1-6 : angle 1.58086 / 0.78 ( 9) link_BETA1-4 : bond 0.00664 / 0.44 ( 14) link_BETA1-4 : angle 2.20896 / 1.48 ( 42) link_NAG-ASN : bond 0.00625 / 0.29 ( 9) link_NAG-ASN : angle 3.31398 / 1.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 69 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1245 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8211 (pp) REVERT: A 2919 ARG cc_start: 0.2837 (OUTLIER) cc_final: 0.1948 (mmm-85) REVERT: A 2936 MET cc_start: 0.6099 (tmm) cc_final: 0.5869 (tmm) REVERT: A 2938 ASP cc_start: -0.0308 (OUTLIER) cc_final: -0.0696 (p0) REVERT: A 2992 MET cc_start: 0.5569 (mmm) cc_final: 0.5296 (mmm) REVERT: A 3092 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.5777 (pmt) REVERT: A 3146 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6650 (pmm) REVERT: A 3150 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6714 (ttt-90) REVERT: A 3275 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7810 (mm-30) REVERT: A 3622 LEU cc_start: 0.7991 (mm) cc_final: 0.7622 (mt) REVERT: A 3664 ASP cc_start: 0.8664 (t0) cc_final: 0.8399 (t0) outliers start: 45 outliers final: 15 residues processed: 102 average time/residue: 0.0921 time to fit residues: 13.9962 Evaluate side-chains 85 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2939 GLU Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3146 MET Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3680 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3770 ASP Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3874 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.153456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107848 restraints weight = 17164.913| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.23 r_work: 0.3350 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10103 Z= 0.174 Angle : 0.688 9.346 13768 Z= 0.338 Chirality : 0.051 0.444 1486 Planarity : 0.004 0.041 1796 Dihedral : 9.433 65.911 1968 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.67 % Allowed : 15.07 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.25), residues: 1180 helix: 0.01 (0.56), residues: 88 sheet: -0.87 (0.42), residues: 164 loop : -0.38 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2993 TYR 0.014 0.002 TYR A3459 PHE 0.017 0.002 PHE A2884 TRP 0.016 0.002 TRP A2925 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (10009) covalent geometry : angle 0.64770 / 0.33 (13559) SS BOND : bond 0.00241 / 0.14 ( 61) SS BOND : angle 1.04305 / 0.79 ( 122) hydrogen bonds : bond 0.04431 / 2.92 ( 203) hydrogen bonds : angle 5.97242 / 4.15 ( 468) Misc. bond : bond 0.00093 / 0.05 ( 4) link_ALPHA1-3 : bond 0.01686 / 0.83 ( 3) link_ALPHA1-3 : angle 2.06823 / 1.10 ( 9) link_ALPHA1-6 : bond 0.01483 / 0.74 ( 3) link_ALPHA1-6 : angle 1.45351 / 0.71 ( 9) link_BETA1-4 : bond 0.00741 / 0.50 ( 14) link_BETA1-4 : angle 2.32805 / 1.70 ( 42) link_NAG-ASN : bond 0.00711 / 0.34 ( 9) link_NAG-ASN : angle 3.87990 / 2.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 59 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5547 (mttt) cc_final: 0.5214 (mmtm) REVERT: A 1230 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8197 (ttm) REVERT: A 1245 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8039 (pp) REVERT: A 2919 ARG cc_start: 0.2699 (OUTLIER) cc_final: 0.1711 (mmm-85) REVERT: A 2961 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6400 (mmt180) REVERT: A 2992 MET cc_start: 0.5529 (mmm) cc_final: 0.5232 (mmm) REVERT: A 3092 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5680 (pmt) REVERT: A 3146 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6774 (pmm) REVERT: A 3150 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6773 (ttt-90) REVERT: A 3275 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 3467 MET cc_start: 0.8407 (mtm) cc_final: 0.8169 (mtt) REVERT: A 3622 LEU cc_start: 0.8148 (mm) cc_final: 0.7679 (mt) REVERT: A 3664 ASP cc_start: 0.8652 (t0) cc_final: 0.8320 (t0) outliers start: 39 outliers final: 20 residues processed: 89 average time/residue: 0.1077 time to fit residues: 13.8128 Evaluate side-chains 84 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain A residue 1230 MET Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2920 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 2961 ARG Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3146 MET Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3228 LEU Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3295 CYS Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3406 ASP Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3695 ILE Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3770 ASP Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3874 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 1 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.154918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109327 restraints weight = 17252.310| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.27 r_work: 0.3369 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10103 Z= 0.131 Angle : 0.653 8.834 13768 Z= 0.322 Chirality : 0.048 0.327 1486 Planarity : 0.004 0.039 1796 Dihedral : 8.826 63.907 1968 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.48 % Allowed : 14.69 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.62 (0.25), residues: 1180 helix: 0.01 (0.56), residues: 88 sheet: -0.87 (0.42), residues: 164 loop : -0.35 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2993 TYR 0.009 0.001 TYR A3459 PHE 0.017 0.002 PHE A2884 TRP 0.010 0.001 TRP A2925 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10009) covalent geometry : angle 0.61858 / 0.31 (13559) SS BOND : bond 0.00277 / 0.14 ( 61) SS BOND : angle 1.13613 / 0.79 ( 122) hydrogen bonds : bond 0.04171 / 2.76 ( 203) hydrogen bonds : angle 5.82053 / 4.04 ( 468) Misc. bond : bond 0.00118 / 0.06 ( 4) link_ALPHA1-3 : bond 0.01634 / 0.80 ( 3) link_ALPHA1-3 : angle 1.89882 / 1.00 ( 9) link_ALPHA1-6 : bond 0.01472 / 0.73 ( 3) link_ALPHA1-6 : angle 1.58639 / 0.78 ( 9) link_BETA1-4 : bond 0.00651 / 0.43 ( 14) link_BETA1-4 : angle 1.98068 / 1.40 ( 42) link_NAG-ASN : bond 0.00587 / 0.29 ( 9) link_NAG-ASN : angle 3.38612 / 2.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5713 (mttt) cc_final: 0.5401 (mmtm) REVERT: A 1245 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8032 (pp) REVERT: A 2919 ARG cc_start: 0.2698 (OUTLIER) cc_final: 0.1718 (mmm-85) REVERT: A 2961 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6445 (mmt180) REVERT: A 2992 MET cc_start: 0.5507 (mmm) cc_final: 0.5182 (mmm) REVERT: A 3092 MET cc_start: 0.5880 (OUTLIER) cc_final: 0.5469 (pmt) REVERT: A 3146 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6751 (pmm) REVERT: A 3150 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6800 (ttt-90) REVERT: A 3664 ASP cc_start: 0.8760 (t0) cc_final: 0.8480 (t0) REVERT: A 3876 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6195 (mm-30) outliers start: 37 outliers final: 21 residues processed: 89 average time/residue: 0.0965 time to fit residues: 12.6444 Evaluate side-chains 88 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2920 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2939 GLU Chi-restraints excluded: chain A residue 2943 HIS Chi-restraints excluded: chain A residue 2961 ARG Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3146 MET Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3404 VAL Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3513 MET Chi-restraints excluded: chain A residue 3636 THR Chi-restraints excluded: chain A residue 3695 ILE Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3859 SER Chi-restraints excluded: chain A residue 3874 ASP Chi-restraints excluded: chain A residue 3876 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 0.0370 chunk 7 optimal weight: 0.0870 chunk 74 optimal weight: 0.0470 overall best weight: 0.1548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.157503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112963 restraints weight = 17150.641| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.28 r_work: 0.3412 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10103 Z= 0.108 Angle : 0.617 9.650 13768 Z= 0.302 Chirality : 0.046 0.275 1486 Planarity : 0.004 0.038 1796 Dihedral : 7.692 59.765 1966 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.20 % Allowed : 15.25 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.25), residues: 1180 helix: -0.03 (0.56), residues: 88 sheet: -0.75 (0.42), residues: 168 loop : -0.29 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2993 TYR 0.009 0.001 TYR D 125 PHE 0.017 0.001 PHE A2884 TRP 0.010 0.001 TRP A3383 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (10009) covalent geometry : angle 0.58884 / 0.30 (13559) SS BOND : bond 0.00223 / 0.11 ( 61) SS BOND : angle 0.92739 / 0.62 ( 122) hydrogen bonds : bond 0.03818 / 2.52 ( 203) hydrogen bonds : angle 5.52687 / 3.82 ( 468) Misc. bond : bond 0.00060 / 0.03 ( 4) link_ALPHA1-3 : bond 0.01633 / 0.79 ( 3) link_ALPHA1-3 : angle 1.76515 / 0.91 ( 9) link_ALPHA1-6 : bond 0.01483 / 0.73 ( 3) link_ALPHA1-6 : angle 1.59113 / 0.79 ( 9) link_BETA1-4 : bond 0.00663 / 0.43 ( 14) link_BETA1-4 : angle 1.78939 / 1.29 ( 42) link_NAG-ASN : bond 0.00606 / 0.29 ( 9) link_NAG-ASN : angle 3.03576 / 1.88 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1245 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8016 (pp) REVERT: A 2919 ARG cc_start: 0.2827 (OUTLIER) cc_final: 0.1947 (mmm-85) REVERT: A 3092 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5274 (pmt) REVERT: A 3135 PHE cc_start: 0.6851 (p90) cc_final: 0.6611 (p90) REVERT: A 3150 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6682 (ttt-90) REVERT: A 3557 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8178 (mm) REVERT: A 3622 LEU cc_start: 0.8054 (mm) cc_final: 0.7596 (mp) REVERT: A 3876 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6857 (mp0) outliers start: 34 outliers final: 19 residues processed: 99 average time/residue: 0.0814 time to fit residues: 11.6847 Evaluate side-chains 84 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2920 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3295 CYS Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3636 THR Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3695 ILE Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3859 SER Chi-restraints excluded: chain A residue 3874 ASP Chi-restraints excluded: chain A residue 3876 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.109646 restraints weight = 17179.129| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.26 r_work: 0.3375 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10103 Z= 0.144 Angle : 0.645 9.194 13768 Z= 0.318 Chirality : 0.048 0.299 1486 Planarity : 0.004 0.042 1796 Dihedral : 7.819 58.515 1966 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.20 % Allowed : 15.54 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.26), residues: 1180 helix: 0.06 (0.56), residues: 88 sheet: -0.78 (0.43), residues: 168 loop : -0.27 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3006 TYR 0.019 0.002 TYR A3244 PHE 0.017 0.002 PHE A2884 TRP 0.009 0.001 TRP A2925 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10009) covalent geometry : angle 0.61671 / 0.31 (13559) SS BOND : bond 0.00221 / 0.13 ( 61) SS BOND : angle 0.93385 / 0.64 ( 122) hydrogen bonds : bond 0.03970 / 2.62 ( 203) hydrogen bonds : angle 5.63783 / 3.88 ( 468) Misc. bond : bond 0.00092 / 0.04 ( 4) link_ALPHA1-3 : bond 0.01547 / 0.75 ( 3) link_ALPHA1-3 : angle 2.07547 / 1.08 ( 9) link_ALPHA1-6 : bond 0.01383 / 0.69 ( 3) link_ALPHA1-6 : angle 1.58940 / 0.78 ( 9) link_BETA1-4 : bond 0.00611 / 0.40 ( 14) link_BETA1-4 : angle 1.80626 / 1.30 ( 42) link_NAG-ASN : bond 0.00529 / 0.27 ( 9) link_NAG-ASN : angle 3.11109 / 1.89 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5701 (mttt) cc_final: 0.5391 (mmtm) REVERT: A 1245 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 2919 ARG cc_start: 0.2886 (OUTLIER) cc_final: 0.1966 (mmm-85) REVERT: A 3092 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.5269 (pmt) REVERT: A 3135 PHE cc_start: 0.6734 (p90) cc_final: 0.6493 (p90) REVERT: A 3150 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6785 (ttt-90) REVERT: A 3392 GLU cc_start: 0.8290 (tt0) cc_final: 0.7936 (mt-10) REVERT: A 3557 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8284 (mm) REVERT: A 3876 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6637 (mm-30) outliers start: 34 outliers final: 22 residues processed: 86 average time/residue: 0.0870 time to fit residues: 11.2889 Evaluate side-chains 87 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2920 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3146 MET Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3228 LEU Chi-restraints excluded: chain A residue 3261 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3295 CYS Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3636 THR Chi-restraints excluded: chain A residue 3695 ILE Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3859 SER Chi-restraints excluded: chain A residue 3874 ASP Chi-restraints excluded: chain A residue 3876 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 4.9990 chunk 99 optimal weight: 0.0670 chunk 9 optimal weight: 0.0370 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2988 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110557 restraints weight = 17092.190| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.23 r_work: 0.3388 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10103 Z= 0.123 Angle : 0.649 10.916 13768 Z= 0.318 Chirality : 0.047 0.295 1486 Planarity : 0.004 0.041 1796 Dihedral : 7.718 58.856 1966 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.73 % Allowed : 16.10 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1180 helix: -0.26 (0.54), residues: 88 sheet: -0.77 (0.43), residues: 168 loop : -0.31 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3006 TYR 0.019 0.001 TYR A3244 PHE 0.017 0.001 PHE A2884 TRP 0.009 0.001 TRP A2925 HIS 0.010 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10009) covalent geometry : angle 0.62342 / 0.31 (13559) SS BOND : bond 0.00203 / 0.11 ( 61) SS BOND : angle 0.92036 / 0.62 ( 122) hydrogen bonds : bond 0.03897 / 2.56 ( 203) hydrogen bonds : angle 5.60868 / 3.86 ( 468) Misc. bond : bond 0.00085 / 0.04 ( 4) link_ALPHA1-3 : bond 0.01582 / 0.77 ( 3) link_ALPHA1-3 : angle 1.93467 / 1.00 ( 9) link_ALPHA1-6 : bond 0.01387 / 0.69 ( 3) link_ALPHA1-6 : angle 1.55898 / 0.77 ( 9) link_BETA1-4 : bond 0.00619 / 0.40 ( 14) link_BETA1-4 : angle 1.75663 / 1.25 ( 42) link_NAG-ASN : bond 0.00545 / 0.27 ( 9) link_NAG-ASN : angle 3.03286 / 1.84 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5810 (mttt) cc_final: 0.5407 (mmtm) REVERT: A 1245 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8041 (pp) REVERT: A 2919 ARG cc_start: 0.2869 (OUTLIER) cc_final: 0.1943 (mmm-85) REVERT: A 3092 MET cc_start: 0.5808 (OUTLIER) cc_final: 0.5274 (pmt) REVERT: A 3135 PHE cc_start: 0.6886 (p90) cc_final: 0.6636 (p90) REVERT: A 3150 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6782 (ttt-90) REVERT: A 3392 GLU cc_start: 0.8261 (tt0) cc_final: 0.7913 (mt-10) REVERT: A 3557 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8291 (mm) REVERT: A 3622 LEU cc_start: 0.8236 (mm) cc_final: 0.7759 (mp) REVERT: A 3713 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: A 3876 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6640 (mm-30) outliers start: 29 outliers final: 21 residues processed: 82 average time/residue: 0.0996 time to fit residues: 11.8375 Evaluate side-chains 84 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2920 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3146 MET Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3228 LEU Chi-restraints excluded: chain A residue 3261 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3295 CYS Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3636 THR Chi-restraints excluded: chain A residue 3695 ILE Chi-restraints excluded: chain A residue 3713 GLU Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3859 SER Chi-restraints excluded: chain A residue 3874 ASP Chi-restraints excluded: chain A residue 3876 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 0.0040 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2988 GLN ** A3782 GLN ** 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 = 0.4100 r_free = 0.4100 target = 0.154121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109146 restraints weight = 17188.671| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.26 r_work: 0.3370 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10103 Z= 0.144 Angle : 0.665 10.804 13768 Z= 0.326 Chirality : 0.048 0.304 1486 Planarity : 0.004 0.043 1796 Dihedral : 7.775 56.168 1966 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.73 % Allowed : 16.10 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.26), residues: 1180 helix: -0.25 (0.54), residues: 88 sheet: -0.80 (0.42), residues: 170 loop : -0.29 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3006 TYR 0.020 0.001 TYR A3244 PHE 0.018 0.002 PHE A2884 TRP 0.011 0.001 TRP A2925 HIS 0.008 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10009) covalent geometry : angle 0.63930 / 0.32 (13559) SS BOND : bond 0.00218 / 0.13 ( 61) SS BOND : angle 0.88423 / 0.59 ( 122) hydrogen bonds : bond 0.03988 / 2.62 ( 203) hydrogen bonds : angle 5.71111 / 3.93 ( 468) Misc. bond : bond 0.00099 / 0.05 ( 4) link_ALPHA1-3 : bond 0.01589 / 0.77 ( 3) link_ALPHA1-3 : angle 2.07188 / 1.07 ( 9) link_ALPHA1-6 : bond 0.01369 / 0.68 ( 3) link_ALPHA1-6 : angle 1.61363 / 0.79 ( 9) link_BETA1-4 : bond 0.00595 / 0.39 ( 14) link_BETA1-4 : angle 1.78782 / 1.29 ( 42) link_NAG-ASN : bond 0.00531 / 0.27 ( 9) link_NAG-ASN : angle 3.12193 / 1.89 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5758 (mttt) cc_final: 0.5382 (mmtm) REVERT: A 1245 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8041 (pp) REVERT: A 2919 ARG cc_start: 0.2703 (OUTLIER) cc_final: 0.1717 (mmm-85) REVERT: A 2961 ARG cc_start: 0.6564 (mmp80) cc_final: 0.6355 (mmp80) REVERT: A 3092 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5244 (pmt) REVERT: A 3135 PHE cc_start: 0.6808 (p90) cc_final: 0.6566 (p90) REVERT: A 3150 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6809 (ttt-90) REVERT: A 3392 GLU cc_start: 0.8270 (tt0) cc_final: 0.7926 (mt-10) REVERT: A 3557 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8332 (mm) REVERT: A 3876 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6661 (mm-30) outliers start: 29 outliers final: 21 residues processed: 80 average time/residue: 0.0872 time to fit residues: 10.2380 Evaluate side-chains 82 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2919 ARG Chi-restraints excluded: chain A residue 2920 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3146 MET Chi-restraints excluded: chain A residue 3150 ARG Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3228 LEU Chi-restraints excluded: chain A residue 3261 THR Chi-restraints excluded: chain A residue 3277 LEU Chi-restraints excluded: chain A residue 3295 CYS Chi-restraints excluded: chain A residue 3329 VAL Chi-restraints excluded: chain A residue 3415 LEU Chi-restraints excluded: chain A residue 3450 THR Chi-restraints excluded: chain A residue 3557 LEU Chi-restraints excluded: chain A residue 3636 THR Chi-restraints excluded: chain A residue 3695 ILE Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3797 MET Chi-restraints excluded: chain A residue 3826 LEU Chi-restraints excluded: chain A residue 3851 CYS Chi-restraints excluded: chain A residue 3859 SER Chi-restraints excluded: chain A residue 3874 ASP Chi-restraints excluded: chain A residue 3876 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 87 optimal weight: 0.0980 chunk 66 optimal weight: 0.1980 chunk 35 optimal weight: 0.0270 chunk 99 optimal weight: 0.0570 chunk 103 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 95 optimal weight: 0.5980 overall best weight: 0.0612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.156764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112639 restraints weight = 17055.920| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.23 r_work: 0.3422 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 10103 Z= 0.111 Angle : 0.633 10.709 13768 Z= 0.311 Chirality : 0.046 0.294 1486 Planarity : 0.004 0.039 1796 Dihedral : 7.294 59.920 1966 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.54 % Allowed : 16.38 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.25), residues: 1180 helix: -0.34 (0.53), residues: 88 sheet: -0.67 (0.43), residues: 168 loop : -0.25 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2966 TYR 0.016 0.001 TYR A3244 PHE 0.018 0.001 PHE A2884 TRP 0.012 0.001 TRP A3383 HIS 0.010 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10009) covalent geometry : angle 0.61077 / 0.31 (13559) SS BOND : bond 0.00169 / 0.09 ( 61) SS BOND : angle 0.78423 / 0.53 ( 122) hydrogen bonds : bond 0.03725 / 2.44 ( 203) hydrogen bonds : angle 5.48344 / 3.78 ( 468) Misc. bond : bond 0.00072 / 0.03 ( 4) link_ALPHA1-3 : bond 0.01634 / 0.79 ( 3) link_ALPHA1-3 : angle 1.78113 / 0.90 ( 9) link_ALPHA1-6 : bond 0.01358 / 0.67 ( 3) link_ALPHA1-6 : angle 1.47909 / 0.73 ( 9) link_BETA1-4 : bond 0.00656 / 0.43 ( 14) link_BETA1-4 : angle 1.65106 / 1.17 ( 42) link_NAG-ASN : bond 0.00598 / 0.28 ( 9) link_NAG-ASN : angle 2.85534 / 1.76 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3461.23 seconds wall clock time: 59 minutes 42.08 seconds (3582.08 seconds total)