Starting phenix.real_space_refine on Sat Aug 23 05:21:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxg_36700/08_2025/8jxg_36700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxg_36700/08_2025/8jxg_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_36700/08_2025/8jxg_36700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxg_36700/08_2025/8jxg_36700.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxg_36700/08_2025/8jxg_36700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxg_36700/08_2025/8jxg_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 105 Unusual residues: {' CA': 21, 'A2G': 4, 'NAG': 2} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.48, per 1000 atoms: 0.25 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: 0.87 Conformation dependent library (CDL) restraints added in 237.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.45 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: 1.88 Time building geometry restraints manager: 1.12 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 2.510 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 2.510 nonbonded pdb=" OD1 ASP A3820 " pdb="CA CA A4725 " model vdw 2.203 2.510 nonbonded pdb=" OD1 ASN A3575 " pdb="CA CA A4719 " model vdw 2.210 2.510 ... (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: 1.630 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 aren 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 covalent geometry : bond 0.00487 (10009) covalent geometry : angle 0.82499 (13559) SS BOND : bond 0.00253 ( 61) SS BOND : angle 0.84833 ( 122) hydrogen bonds : bond 0.26383 ( 203) hydrogen bonds : angle 9.66975 ( 468) Misc. bond : bond 0.24207 ( 4) link_ALPHA1-3 : bond 0.01130 ( 3) link_ALPHA1-3 : angle 1.41038 ( 9) link_ALPHA1-6 : bond 0.00731 ( 3) link_ALPHA1-6 : angle 1.00971 ( 9) link_BETA1-4 : bond 0.00747 ( 14) link_BETA1-4 : angle 1.93029 ( 42) link_NAG-ASN : bond 0.00965 ( 9) link_NAG-ASN : angle 4.06253 ( 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 : 0.351 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: 0.0744 time to fit residues: 9.8077 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 : 0.280 ------------------------------------------------------------------------------- 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: 0.4980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 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: 0.4980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.2980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.154865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110141 restraints weight = 17049.830| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.58 r_work: 0.3354 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10103 Z= 0.135 Angle : 0.715 10.143 13768 Z= 0.347 Chirality : 0.049 0.323 1486 Planarity : 0.004 0.039 1796 Dihedral : 14.015 91.515 1995 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.39 % Allowed : 14.60 % 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 aren not related in a simple way. whole: -0.69 (0.24), residues: 1180 helix: -0.44 (0.53), residues: 87 sheet: -0.82 (0.40), residues: 164 loop : -0.38 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 78 TYR 0.010 0.001 TYR A3244 PHE 0.017 0.002 PHE A2884 TRP 0.018 0.001 TRP D 66 HIS 0.009 0.001 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00282 (10009) covalent geometry : angle 0.67250 (13559) SS BOND : bond 0.00190 ( 61) SS BOND : angle 0.78614 ( 122) hydrogen bonds : bond 0.05284 ( 203) hydrogen bonds : angle 6.57540 ( 468) Misc. bond : bond 0.00201 ( 4) link_ALPHA1-3 : bond 0.01674 ( 3) link_ALPHA1-3 : angle 1.94386 ( 9) link_ALPHA1-6 : bond 0.01270 ( 3) link_ALPHA1-6 : angle 1.88106 ( 9) link_BETA1-4 : bond 0.00736 ( 14) link_BETA1-4 : angle 2.54514 ( 42) link_NAG-ASN : bond 0.00777 ( 9) link_NAG-ASN : angle 4.23245 ( 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 108 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5539 (mttt) cc_final: 0.5079 (mmtm) REVERT: A 1230 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8206 (ttm) REVERT: A 2919 ARG cc_start: 0.2617 (OUTLIER) cc_final: 0.1781 (mtp85) REVERT: A 2961 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6337 (mmt180) REVERT: A 2992 MET cc_start: 0.4918 (mmm) cc_final: 0.4702 (mmm) REVERT: A 3275 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 3664 ASP cc_start: 0.8576 (t0) cc_final: 0.8286 (t0) REVERT: A 3807 CYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7428 (m) outliers start: 36 outliers final: 21 residues processed: 96 average time/residue: 0.0748 time to fit residues: 10.5551 Evaluate side-chains 87 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 2971 TYR Chi-restraints excluded: chain A residue 3096 CYS 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 40.0000 chunk 93 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4097 r_free = 0.4097 target = 0.153920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110816 restraints weight = 17153.842| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.67 r_work: 0.3336 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10103 Z= 0.141 Angle : 0.673 9.526 13768 Z= 0.328 Chirality : 0.049 0.307 1486 Planarity : 0.004 0.038 1796 Dihedral : 11.755 80.046 1973 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.48 % Allowed : 14.41 % 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 aren not related in a simple way. whole: -0.68 (0.25), residues: 1180 helix: -0.34 (0.55), residues: 89 sheet: -0.89 (0.41), residues: 164 loop : -0.36 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3350 TYR 0.015 0.002 TYR D 125 PHE 0.016 0.002 PHE A3418 TRP 0.011 0.001 TRP D 66 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00314 (10009) covalent geometry : angle 0.63500 (13559) SS BOND : bond 0.00210 ( 61) SS BOND : angle 0.89370 ( 122) hydrogen bonds : bond 0.04910 ( 203) hydrogen bonds : angle 6.17974 ( 468) Misc. bond : bond 0.00069 ( 4) link_ALPHA1-3 : bond 0.01811 ( 3) link_ALPHA1-3 : angle 1.62893 ( 9) link_ALPHA1-6 : bond 0.01406 ( 3) link_ALPHA1-6 : angle 1.61875 ( 9) link_BETA1-4 : bond 0.00686 ( 14) link_BETA1-4 : angle 2.50736 ( 42) link_NAG-ASN : bond 0.00655 ( 9) link_NAG-ASN : angle 3.63870 ( 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 103 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5671 (mttt) cc_final: 0.5347 (mmtm) REVERT: A 2919 ARG cc_start: 0.2805 (OUTLIER) cc_final: 0.1997 (mtp85) REVERT: A 2961 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6345 (mmt180) REVERT: A 3146 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6644 (pmm) REVERT: A 3150 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6799 (ttt-90) REVERT: A 3275 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 3664 ASP cc_start: 0.8696 (t0) cc_final: 0.8454 (t0) outliers start: 37 outliers final: 25 residues processed: 95 average time/residue: 0.0902 time to fit residues: 12.2969 Evaluate side-chains 93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 1238 CYS 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 2971 TYR Chi-restraints excluded: chain A residue 2993 ARG Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3096 CYS 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 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 3578 GLN 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 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: 0.5980 chunk 35 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.154352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108412 restraints weight = 17404.567| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.21 r_work: 0.3359 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10103 Z= 0.133 Angle : 0.650 8.612 13768 Z= 0.317 Chirality : 0.049 0.288 1486 Planarity : 0.004 0.038 1796 Dihedral : 10.188 69.048 1971 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.86 % Allowed : 14.78 % 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 aren not related in a simple way. whole: -0.63 (0.25), residues: 1180 helix: -0.25 (0.54), residues: 94 sheet: -0.84 (0.42), residues: 164 loop : -0.34 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3212 TYR 0.010 0.001 TYR A3459 PHE 0.016 0.002 PHE A2884 TRP 0.010 0.001 TRP A3383 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00293 (10009) covalent geometry : angle 0.61591 (13559) SS BOND : bond 0.00197 ( 61) SS BOND : angle 0.82483 ( 122) hydrogen bonds : bond 0.04278 ( 203) hydrogen bonds : angle 5.94335 ( 468) Misc. bond : bond 0.00138 ( 4) link_ALPHA1-3 : bond 0.01770 ( 3) link_ALPHA1-3 : angle 1.84309 ( 9) link_ALPHA1-6 : bond 0.01499 ( 3) link_ALPHA1-6 : angle 1.48240 ( 9) link_BETA1-4 : bond 0.00650 ( 14) link_BETA1-4 : angle 2.29271 ( 42) link_NAG-ASN : bond 0.00563 ( 9) link_NAG-ASN : angle 3.47067 ( 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 109 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 68 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5658 (mttt) cc_final: 0.5371 (mmtm) REVERT: A 1230 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8330 (ttm) REVERT: A 1245 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8366 (pp) REVERT: A 2919 ARG cc_start: 0.2663 (OUTLIER) cc_final: 0.1697 (mmm-85) REVERT: A 3092 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.5627 (pmt) REVERT: A 3146 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6761 (pmm) REVERT: A 3150 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6741 (ttt-90) REVERT: A 3275 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 3622 LEU cc_start: 0.8071 (mm) cc_final: 0.7651 (mt) REVERT: A 3664 ASP cc_start: 0.8646 (t0) cc_final: 0.8415 (t0) outliers start: 41 outliers final: 23 residues processed: 95 average time/residue: 0.0838 time to fit residues: 11.4727 Evaluate side-chains 93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 1238 CYS Chi-restraints excluded: chain A residue 1245 ILE 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 2971 TYR 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 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 3549 LEU Chi-restraints excluded: chain A residue 3578 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 0.0270 chunk 77 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4104 r_free = 0.4104 target = 0.154543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111314 restraints weight = 17199.736| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.75 r_work: 0.3344 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10103 Z= 0.124 Angle : 0.625 8.494 13768 Z= 0.307 Chirality : 0.048 0.285 1486 Planarity : 0.004 0.040 1796 Dihedral : 9.360 66.443 1970 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.86 % Allowed : 14.88 % 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 aren not related in a simple way. whole: -0.55 (0.25), residues: 1180 helix: -0.15 (0.55), residues: 94 sheet: -0.76 (0.42), residues: 164 loop : -0.29 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2993 TYR 0.010 0.001 TYR A3459 PHE 0.015 0.002 PHE A2884 TRP 0.009 0.001 TRP A3383 HIS 0.005 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00270 (10009) covalent geometry : angle 0.59302 (13559) SS BOND : bond 0.00187 ( 61) SS BOND : angle 0.84723 ( 122) hydrogen bonds : bond 0.04114 ( 203) hydrogen bonds : angle 5.81112 ( 468) Misc. bond : bond 0.00165 ( 4) link_ALPHA1-3 : bond 0.01751 ( 3) link_ALPHA1-3 : angle 1.90018 ( 9) link_ALPHA1-6 : bond 0.01485 ( 3) link_ALPHA1-6 : angle 1.42638 ( 9) link_BETA1-4 : bond 0.00647 ( 14) link_BETA1-4 : angle 2.07954 ( 42) link_NAG-ASN : bond 0.00568 ( 9) link_NAG-ASN : angle 3.29425 ( 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 110 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5650 (mttt) cc_final: 0.5367 (mmtm) REVERT: D 89 GLN cc_start: 0.7315 (tt0) cc_final: 0.7098 (tt0) REVERT: A 1230 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8297 (ttm) REVERT: A 1245 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8241 (pp) REVERT: A 2919 ARG cc_start: 0.2856 (OUTLIER) cc_final: 0.1936 (mmm-85) REVERT: A 3092 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5718 (pmt) REVERT: A 3146 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6793 (pmm) REVERT: A 3150 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6799 (ttt-90) REVERT: A 3275 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 3622 LEU cc_start: 0.8107 (mm) cc_final: 0.7659 (mt) REVERT: A 3664 ASP cc_start: 0.8675 (t0) cc_final: 0.8436 (t0) outliers start: 41 outliers final: 23 residues processed: 96 average time/residue: 0.1012 time to fit residues: 13.7864 Evaluate side-chains 96 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 1238 CYS Chi-restraints excluded: chain A residue 1245 ILE 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 2971 TYR Chi-restraints excluded: chain A residue 3020 CYS 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 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 3406 ASP 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 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 3859 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 104 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4099 r_free = 0.4099 target = 0.154067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108995 restraints weight = 17305.795| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.64 r_work: 0.3332 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10103 Z= 0.137 Angle : 0.642 10.283 13768 Z= 0.312 Chirality : 0.048 0.422 1486 Planarity : 0.004 0.042 1796 Dihedral : 8.817 63.521 1968 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.05 % Allowed : 15.07 % Favored : 80.89 % 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 aren not related in a simple way. whole: -0.51 (0.25), residues: 1180 helix: -0.04 (0.55), residues: 94 sheet: -0.79 (0.42), residues: 164 loop : -0.26 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3738 TYR 0.011 0.001 TYR A3459 PHE 0.015 0.002 PHE A2884 TRP 0.007 0.001 TRP A3383 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00305 (10009) covalent geometry : angle 0.60453 (13559) SS BOND : bond 0.00198 ( 61) SS BOND : angle 0.73161 ( 122) hydrogen bonds : bond 0.04058 ( 203) hydrogen bonds : angle 5.78794 ( 468) Misc. bond : bond 0.00130 ( 4) link_ALPHA1-3 : bond 0.01683 ( 3) link_ALPHA1-3 : angle 2.02660 ( 9) link_ALPHA1-6 : bond 0.01450 ( 3) link_ALPHA1-6 : angle 1.57447 ( 9) link_BETA1-4 : bond 0.00780 ( 14) link_BETA1-4 : angle 2.09947 ( 42) link_NAG-ASN : bond 0.00796 ( 9) link_NAG-ASN : angle 3.92374 ( 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 108 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 65 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5657 (mttt) cc_final: 0.5360 (mmtm) REVERT: A 1230 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8295 (ttm) REVERT: A 1245 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8153 (pp) REVERT: A 2919 ARG cc_start: 0.2712 (OUTLIER) cc_final: 0.1744 (mmm-85) REVERT: A 3017 ARG cc_start: 0.7119 (mpp-170) cc_final: 0.6895 (mtm-85) REVERT: A 3092 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.5677 (pmt) REVERT: A 3146 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6791 (pmm) REVERT: A 3150 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6806 (ttt-90) REVERT: A 3261 THR cc_start: 0.9024 (t) cc_final: 0.8776 (p) REVERT: A 3664 ASP cc_start: 0.8695 (t0) cc_final: 0.8446 (t0) outliers start: 43 outliers final: 24 residues processed: 95 average time/residue: 0.0860 time to fit residues: 11.7429 Evaluate side-chains 93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 2927 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 2971 TYR 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 3513 MET 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 3859 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 0.0670 chunk 116 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 78 optimal weight: 0.0870 chunk 7 optimal weight: 0.0010 chunk 74 optimal weight: 0.9990 overall best weight: 0.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.156008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111784 restraints weight = 17295.111| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.68 r_work: 0.3371 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10103 Z= 0.109 Angle : 0.612 9.160 13768 Z= 0.299 Chirality : 0.047 0.351 1486 Planarity : 0.004 0.039 1796 Dihedral : 8.189 61.873 1968 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.58 % Allowed : 15.25 % Favored : 81.17 % 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 aren not related in a simple way. whole: -0.39 (0.26), residues: 1180 helix: 0.23 (0.57), residues: 88 sheet: -0.72 (0.42), residues: 164 loop : -0.18 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2993 TYR 0.007 0.001 TYR A3136 PHE 0.015 0.001 PHE A2884 TRP 0.009 0.001 TRP A3383 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00224 (10009) covalent geometry : angle 0.58048 (13559) SS BOND : bond 0.00180 ( 61) SS BOND : angle 0.75488 ( 122) hydrogen bonds : bond 0.03859 ( 203) hydrogen bonds : angle 5.59210 ( 468) Misc. bond : bond 0.00122 ( 4) link_ALPHA1-3 : bond 0.01639 ( 3) link_ALPHA1-3 : angle 1.77865 ( 9) link_ALPHA1-6 : bond 0.01491 ( 3) link_ALPHA1-6 : angle 1.62962 ( 9) link_BETA1-4 : bond 0.00680 ( 14) link_BETA1-4 : angle 1.87215 ( 42) link_NAG-ASN : bond 0.00642 ( 9) link_NAG-ASN : angle 3.42696 ( 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 112 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5602 (mttt) cc_final: 0.5348 (mmtm) REVERT: A 1245 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8132 (pp) REVERT: A 2919 ARG cc_start: 0.2859 (OUTLIER) cc_final: 0.1977 (mmm-85) REVERT: A 3092 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5662 (pmt) REVERT: A 3146 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6865 (pmm) REVERT: A 3150 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6734 (ttt-90) REVERT: A 3261 THR cc_start: 0.8950 (t) cc_final: 0.8724 (p) REVERT: A 3295 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8127 (t) REVERT: A 3557 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8148 (mm) REVERT: A 3622 LEU cc_start: 0.8093 (mm) cc_final: 0.7644 (mp) outliers start: 38 outliers final: 20 residues processed: 102 average time/residue: 0.1062 time to fit residues: 15.4487 Evaluate side-chains 95 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain A residue 1238 CYS Chi-restraints excluded: chain A residue 1239 GLN 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 2927 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 2971 TYR Chi-restraints excluded: chain A residue 3020 CYS 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 74 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.4980 chunk 78 optimal weight: 0.0070 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 HIS ** 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 = 0.4120 r_free = 0.4120 target = 0.155820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111874 restraints weight = 17162.860| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.76 r_work: 0.3359 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10103 Z= 0.113 Angle : 0.621 9.551 13768 Z= 0.307 Chirality : 0.047 0.321 1486 Planarity : 0.004 0.040 1796 Dihedral : 7.936 60.111 1966 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.20 % Allowed : 15.35 % Favored : 81.45 % 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 aren not related in a simple way. whole: -0.37 (0.26), residues: 1180 helix: 0.24 (0.56), residues: 88 sheet: -0.67 (0.42), residues: 168 loop : -0.18 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3017 TYR 0.016 0.001 TYR A3244 PHE 0.014 0.001 PHE A2884 TRP 0.008 0.001 TRP A3383 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00244 (10009) covalent geometry : angle 0.59143 (13559) SS BOND : bond 0.00222 ( 61) SS BOND : angle 0.88623 ( 122) hydrogen bonds : bond 0.03767 ( 203) hydrogen bonds : angle 5.53181 ( 468) Misc. bond : bond 0.00103 ( 4) link_ALPHA1-3 : bond 0.01600 ( 3) link_ALPHA1-3 : angle 1.85381 ( 9) link_ALPHA1-6 : bond 0.01447 ( 3) link_ALPHA1-6 : angle 1.57734 ( 9) link_BETA1-4 : bond 0.00643 ( 14) link_BETA1-4 : angle 1.82360 ( 42) link_NAG-ASN : bond 0.00588 ( 9) link_NAG-ASN : angle 3.25557 ( 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 104 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5695 (mttt) cc_final: 0.5393 (mmtm) REVERT: A 1230 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8263 (ttm) REVERT: A 1245 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8199 (pp) REVERT: A 2919 ARG cc_start: 0.2851 (OUTLIER) cc_final: 0.1947 (mmm-85) REVERT: A 3092 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5708 (pmt) REVERT: A 3135 PHE cc_start: 0.6731 (p90) cc_final: 0.6471 (p90) REVERT: A 3146 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6893 (pmm) REVERT: A 3150 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6760 (ttt-90) REVERT: A 3261 THR cc_start: 0.8979 (t) cc_final: 0.8716 (p) REVERT: A 3379 ASP cc_start: 0.8569 (p0) cc_final: 0.8351 (m-30) REVERT: A 3557 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8192 (mm) REVERT: A 3622 LEU cc_start: 0.8111 (mm) cc_final: 0.7647 (mp) outliers start: 34 outliers final: 22 residues processed: 94 average time/residue: 0.1161 time to fit residues: 15.3602 Evaluate side-chains 95 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 2927 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 2971 TYR Chi-restraints excluded: chain A residue 3020 CYS Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3145 LEU 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 HIS ** 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 = 0.155024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111405 restraints weight = 17309.956| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.70 r_work: 0.3347 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10103 Z= 0.127 Angle : 0.629 9.474 13768 Z= 0.310 Chirality : 0.047 0.316 1486 Planarity : 0.004 0.042 1796 Dihedral : 7.824 58.988 1966 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.92 % Allowed : 15.91 % 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 aren not related in a simple way. whole: -0.45 (0.26), residues: 1180 helix: -0.03 (0.55), residues: 94 sheet: -0.68 (0.43), residues: 168 loop : -0.22 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3006 TYR 0.020 0.001 TYR A3244 PHE 0.015 0.002 PHE A2884 TRP 0.009 0.001 TRP A3245 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00283 (10009) covalent geometry : angle 0.60016 (13559) SS BOND : bond 0.00203 ( 61) SS BOND : angle 0.83997 ( 122) hydrogen bonds : bond 0.03841 ( 203) hydrogen bonds : angle 5.55731 ( 468) Misc. bond : bond 0.00104 ( 4) link_ALPHA1-3 : bond 0.01590 ( 3) link_ALPHA1-3 : angle 1.96492 ( 9) link_ALPHA1-6 : bond 0.01395 ( 3) link_ALPHA1-6 : angle 1.57811 ( 9) link_BETA1-4 : bond 0.00619 ( 14) link_BETA1-4 : angle 1.80356 ( 42) link_NAG-ASN : bond 0.00554 ( 9) link_NAG-ASN : angle 3.21272 ( 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 97 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5751 (mttt) cc_final: 0.5377 (mmtm) REVERT: A 1230 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8244 (ttm) REVERT: A 1245 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8138 (pp) REVERT: A 2919 ARG cc_start: 0.2870 (OUTLIER) cc_final: 0.1984 (mmm-85) REVERT: A 3092 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5646 (pmt) REVERT: A 3135 PHE cc_start: 0.6736 (p90) cc_final: 0.6466 (p90) REVERT: A 3146 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6879 (pmm) REVERT: A 3150 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6763 (ttt-90) REVERT: A 3261 THR cc_start: 0.9010 (t) cc_final: 0.8763 (p) REVERT: A 3392 GLU cc_start: 0.8291 (tt0) cc_final: 0.7930 (mt-10) REVERT: A 3557 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 3577 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7872 (mtm-85) outliers start: 31 outliers final: 21 residues processed: 89 average time/residue: 0.1171 time to fit residues: 14.6360 Evaluate side-chains 92 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 2927 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 2971 TYR Chi-restraints excluded: chain A residue 3020 CYS 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 76 optimal weight: 0.0670 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 HIS ** 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 = 0.4105 r_free = 0.4105 target = 0.154623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109853 restraints weight = 17221.361| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.62 r_work: 0.3348 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10103 Z= 0.129 Angle : 0.635 9.899 13768 Z= 0.312 Chirality : 0.047 0.315 1486 Planarity : 0.004 0.042 1796 Dihedral : 7.728 58.076 1966 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.92 % Allowed : 15.82 % 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 aren not related in a simple way. whole: -0.49 (0.25), residues: 1180 helix: -0.10 (0.53), residues: 97 sheet: -0.71 (0.42), residues: 168 loop : -0.24 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2961 TYR 0.021 0.001 TYR A3244 PHE 0.015 0.002 PHE A2884 TRP 0.009 0.001 TRP A3245 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00290 (10009) covalent geometry : angle 0.60812 (13559) SS BOND : bond 0.00188 ( 61) SS BOND : angle 0.78649 ( 122) hydrogen bonds : bond 0.03814 ( 203) hydrogen bonds : angle 5.58827 ( 468) Misc. bond : bond 0.00105 ( 4) link_ALPHA1-3 : bond 0.01584 ( 3) link_ALPHA1-3 : angle 1.95808 ( 9) link_ALPHA1-6 : bond 0.01364 ( 3) link_ALPHA1-6 : angle 1.56510 ( 9) link_BETA1-4 : bond 0.00609 ( 14) link_BETA1-4 : angle 1.75740 ( 42) link_NAG-ASN : bond 0.00557 ( 9) link_NAG-ASN : angle 3.16285 ( 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 98 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: D 70 LYS cc_start: 0.5684 (mttt) cc_final: 0.5332 (mmtm) REVERT: A 1230 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8310 (ttm) REVERT: A 1245 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8116 (pp) REVERT: A 2919 ARG cc_start: 0.2682 (OUTLIER) cc_final: 0.1728 (mmm-85) REVERT: A 3017 ARG cc_start: 0.6681 (mpp-170) cc_final: 0.6404 (mpp-170) REVERT: A 3092 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.5651 (pmt) REVERT: A 3135 PHE cc_start: 0.6891 (p90) cc_final: 0.6628 (p90) REVERT: A 3146 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6865 (pmm) REVERT: A 3150 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6779 (ttt-90) REVERT: A 3261 THR cc_start: 0.8996 (t) cc_final: 0.8758 (p) REVERT: A 3392 GLU cc_start: 0.8289 (tt0) cc_final: 0.7931 (mt-10) REVERT: A 3557 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8176 (mm) REVERT: A 3577 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7853 (mtm-85) REVERT: A 3622 LEU cc_start: 0.8276 (mm) cc_final: 0.7796 (mp) outliers start: 31 outliers final: 22 residues processed: 89 average time/residue: 0.1084 time to fit residues: 13.7923 Evaluate side-chains 95 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 2927 CYS Chi-restraints excluded: chain A residue 2938 ASP Chi-restraints excluded: chain A residue 2944 HIS Chi-restraints excluded: chain A residue 2971 TYR Chi-restraints excluded: chain A residue 3020 CYS Chi-restraints excluded: chain A residue 3086 ASN Chi-restraints excluded: chain A residue 3092 MET Chi-restraints excluded: chain A residue 3145 LEU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 0.3980 chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 11 optimal weight: 0.0170 chunk 95 optimal weight: 0.0070 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4108 r_free = 0.4108 target = 0.154820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.111373 restraints weight = 17150.481| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.68 r_work: 0.3355 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10103 Z= 0.118 Angle : 0.622 10.122 13768 Z= 0.305 Chirality : 0.046 0.307 1486 Planarity : 0.004 0.041 1796 Dihedral : 7.461 59.686 1966 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.01 % Allowed : 15.63 % 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 aren not related in a simple way. whole: -0.44 (0.25), residues: 1180 helix: -0.05 (0.53), residues: 94 sheet: -0.69 (0.42), residues: 168 loop : -0.20 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3017 TYR 0.021 0.001 TYR A3244 PHE 0.015 0.001 PHE A2884 TRP 0.010 0.001 TRP A3245 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00263 (10009) covalent geometry : angle 0.59623 (13559) SS BOND : bond 0.00181 ( 61) SS BOND : angle 0.75195 ( 122) hydrogen bonds : bond 0.03727 ( 203) hydrogen bonds : angle 5.50485 ( 468) Misc. bond : bond 0.00103 ( 4) link_ALPHA1-3 : bond 0.01596 ( 3) link_ALPHA1-3 : angle 1.92418 ( 9) link_ALPHA1-6 : bond 0.01353 ( 3) link_ALPHA1-6 : angle 1.53951 ( 9) link_BETA1-4 : bond 0.00616 ( 14) link_BETA1-4 : angle 1.70046 ( 42) link_NAG-ASN : bond 0.00554 ( 9) link_NAG-ASN : angle 3.07273 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3519.30 seconds wall clock time: 60 minutes 36.93 seconds (3636.93 seconds total)