Starting phenix.real_space_refine on Sat Aug 23 12:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxa_36694/08_2025/8jxa_36694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxa_36694/08_2025/8jxa_36694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jxa_36694/08_2025/8jxa_36694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxa_36694/08_2025/8jxa_36694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jxa_36694/08_2025/8jxa_36694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxa_36694/08_2025/8jxa_36694.map" } resolution = 3.8 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 20 9.91 5 S 149 5.16 5 C 7232 2.51 5 N 2061 2.21 5 O 2427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s 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: 11889 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8455 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 53, 'TRANS': 1023} Chain breaks: 1 Chain: "B" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2904 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 20, 'TRANS': 340} 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: "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: "D" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 118 Unusual residues: {' CA': 20, 'A2G': 5, 'NAG': 2} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.69, per 1000 atoms: 0.23 Number of scatterers: 11889 At special positions: 0 Unit cell: (114.291, 117.113, 165.087, 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 20 19.99 S 149 16.00 O 2427 8.00 N 2061 7.00 C 7232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=64, 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 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=2.03 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=2.04 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=2.03 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=2.02 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 Simple disulfide: pdb=" SG CYS B4336 " - pdb=" SG CYS B4344 " distance=2.03 Simple disulfide: pdb=" SG CYS B4340 " - pdb=" SG CYS B4353 " distance=2.03 Simple disulfide: pdb=" SG CYS B4355 " - pdb=" SG CYS B4369 " distance=2.03 Simple disulfide: pdb=" SG CYS B4383 " - pdb=" SG CYS B4391 " distance=2.03 Simple disulfide: pdb=" SG CYS B4385 " - pdb=" SG CYS B4401 " distance=2.03 Simple disulfide: pdb=" SG CYS B4403 " - pdb=" SG CYS B4412 " 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=5, 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 " BETA1-3 " NAG K 2 " - " BMA K 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A4701 " - " ASN A3448 " " NAG A4702 " - " ASN A3682 " " NAG C 1 " - " ASN A3127 " " NAG D 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=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 388.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 33 sheets defined 10.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 1246 through 1250 Processing helix chain 'A' and resid 1260 through 1264 removed outlier: 3.665A pdb=" N GLU A1263 " --> pdb=" O GLY A1260 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS A1264 " --> pdb=" O SER A1261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1260 through 1264' Processing helix chain 'A' and resid 2924 through 2926 No H-bonds generated for 'chain 'A' and resid 2924 through 2926' Processing helix chain 'A' and resid 2940 through 2944 Processing helix chain 'A' and resid 2962 through 2966 removed outlier: 3.951A pdb=" N ARG A2966 " --> pdb=" O PRO A2963 " (cutoff:3.500A) Processing helix chain 'A' and resid 2984 through 2989 removed outlier: 4.506A pdb=" N ASN A2989 " --> pdb=" O ASP A2985 " (cutoff:3.500A) Processing helix chain 'A' and resid 3009 through 3013 removed outlier: 3.513A pdb=" N PHE A3012 " --> pdb=" O ARG A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3091 through 3095 Processing helix chain 'A' and resid 3156 through 3161 Processing helix chain 'A' and resid 3162 through 3165 removed outlier: 3.570A 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 removed outlier: 3.612A pdb=" N GLN A3464 " --> pdb=" O PRO A3461 " (cutoff:3.500A) 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 removed outlier: 3.555A pdb=" N CYS A3591 " --> pdb=" O ASP A3587 " (cutoff:3.500A) Processing helix chain 'A' and resid 3612 through 3614 No H-bonds generated for 'chain 'A' and resid 3612 through 3614' Processing helix chain 'A' and resid 3628 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: 3.719A 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 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 removed outlier: 3.567A pdb=" N ARG A3793 " --> pdb=" O SER A3790 " (cutoff:3.500A) 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 3828 through 3832 removed outlier: 3.603A pdb=" N GLU A3831 " --> pdb=" O ALA A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3858 through 3862 Processing helix chain 'A' and resid 3900 through 3904 Processing helix chain 'A' and resid 3914 through 3918 Processing helix chain 'B' and resid 4324 through 4328 Processing sheet with id=AA1, first strand: chain 'A' and resid 1236 through 1237 Processing sheet with id=AA2, first strand: chain 'A' and resid 2912 through 2914 Processing sheet with id=AA3, first strand: chain 'A' and resid 3038 through 3040 Processing sheet with id=AA4, first strand: chain 'A' and resid 3082 through 3084 removed outlier: 3.588A pdb=" N HIS A3088 " --> pdb=" O CYS A3084 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3127 through 3131 removed outlier: 3.904A pdb=" N SER A3138 " --> pdb=" O ASN A3127 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A3129 " --> pdb=" O TYR A3136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3143 through 3145 Processing sheet with id=AA7, first strand: chain 'A' and resid 3168 through 3172 Processing sheet with id=AA8, first strand: chain 'A' and resid 3184 through 3186 Processing sheet with id=AA9, first strand: chain 'A' and resid 3221 through 3226 removed outlier: 6.453A pdb=" N ILE A3211 " --> pdb=" O ILE A3224 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A3202 " --> pdb=" O TYR A3459 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A3455 " --> pdb=" O SER A3206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3234 through 3237 removed outlier: 6.792A pdb=" N ILE A3253 " --> pdb=" O ILE A3266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3274 through 3280 removed outlier: 4.062A pdb=" N SER A3276 " --> pdb=" O LEU A3289 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TRP A3288 " --> pdb=" O PHE A3297 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A3296 " --> pdb=" O ILE A3309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3325 through 3331 removed outlier: 5.271A pdb=" N GLY A3327 " --> pdb=" O ALA A3340 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A3348 " --> pdb=" O ILE A3361 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3371 through 3375 removed outlier: 3.783A pdb=" N ALA A3371 " --> pdb=" O ALA A3384 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A3384 " --> pdb=" O ALA A3371 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A3391 " --> pdb=" O VAL A3404 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3412 through 3418 removed outlier: 3.990A pdb=" N ALA A3414 " --> pdb=" O THR A3425 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A3432 " --> pdb=" O LEU A3446 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3482 through 3484 Processing sheet with id=AB7, first strand: chain 'A' and resid 3499 through 3503 removed outlier: 3.561A pdb=" N MET A3511 " --> pdb=" O GLN A3500 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3518 through 3520 Processing sheet with id=AB9, first strand: chain 'A' and resid 3560 through 3561 Processing sheet with id=AC1, first strand: chain 'A' and resid 3600 through 3602 Processing sheet with id=AC2, first strand: chain 'A' and resid 3641 through 3643 Processing sheet with id=AC3, first strand: chain 'A' and resid 3685 through 3687 Processing sheet with id=AC4, first strand: chain 'A' and resid 3726 through 3728 Processing sheet with id=AC5, first strand: chain 'A' and resid 3765 through 3767 Processing sheet with id=AC6, first strand: chain 'A' and resid 3804 through 3806 Processing sheet with id=AC7, first strand: chain 'A' and resid 3849 through 3850 Processing sheet with id=AC8, first strand: chain 'B' and resid 4076 through 4077 removed outlier: 3.533A pdb=" N SER B4077 " --> pdb=" O LYS B4068 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS B4068 " --> pdb=" O SER B4077 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 4086 through 4092 removed outlier: 4.227A pdb=" N THR B4088 " --> pdb=" O THR B4106 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B4136 " --> pdb=" O ARG B4119 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 4148 through 4152 removed outlier: 3.608A pdb=" N GLY B4148 " --> pdb=" O SER B4161 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS B4157 " --> pdb=" O ASP B4152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 4189 through 4195 removed outlier: 5.135A pdb=" N ALA B4191 " --> pdb=" O THR B4204 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B4204 " --> pdb=" O ALA B4191 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 4236 through 4239 removed outlier: 6.981A pdb=" N ILE B4256 " --> pdb=" O ILE B4269 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 4276 through 4282 removed outlier: 4.814A pdb=" N SER B4278 " --> pdb=" O VAL B4289 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B4289 " --> pdb=" O SER B4278 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B4295 " --> pdb=" O ALA B4290 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B4296 " --> pdb=" O VAL B4310 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 4343 through 4347 Processing sheet with id=AD6, first strand: chain 'B' and resid 4390 through 4393 232 hydrogen bonds defined for protein. 507 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: 1.95 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4014 1.34 - 1.46: 2534 1.46 - 1.58: 5433 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 12149 Sorted by residual: bond pdb=" N LEU A3622 " pdb=" CA LEU A3622 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.60e+00 bond pdb=" N CYS A3313 " pdb=" CA CYS A3313 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.33e-02 5.65e+03 6.57e+00 bond pdb=" N SER A3299 " pdb=" CA SER A3299 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.12e+00 bond pdb=" N HIS A3305 " pdb=" CA HIS A3305 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.96e+00 bond pdb=" N ASP A3315 " pdb=" CA ASP A3315 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.62e+00 ... (remaining 12144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 15817 1.94 - 3.88: 592 3.88 - 5.83: 57 5.83 - 7.77: 6 7.77 - 9.71: 3 Bond angle restraints: 16475 Sorted by residual: angle pdb=" N THR A3319 " pdb=" CA THR A3319 " pdb=" C THR A3319 " ideal model delta sigma weight residual 112.89 107.99 4.90 1.24e+00 6.50e-01 1.56e+01 angle pdb=" N VAL B4339 " pdb=" CA VAL B4339 " pdb=" C VAL B4339 " ideal model delta sigma weight residual 113.42 109.05 4.37 1.17e+00 7.31e-01 1.39e+01 angle pdb=" N GLY A3901 " pdb=" CA GLY A3901 " pdb=" C GLY A3901 " ideal model delta sigma weight residual 111.02 117.77 -6.75 1.86e+00 2.89e-01 1.32e+01 angle pdb=" CA MET A3513 " pdb=" CB MET A3513 " pdb=" CG MET A3513 " ideal model delta sigma weight residual 114.10 121.20 -7.10 2.00e+00 2.50e-01 1.26e+01 angle pdb=" N LEU A3301 " pdb=" CA LEU A3301 " pdb=" C LEU A3301 " ideal model delta sigma weight residual 112.87 108.83 4.04 1.20e+00 6.94e-01 1.13e+01 ... (remaining 16470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 7118 21.78 - 43.55: 605 43.55 - 65.33: 131 65.33 - 87.10: 58 87.10 - 108.88: 26 Dihedral angle restraints: 7938 sinusoidal: 3764 harmonic: 4174 Sorted by residual: dihedral pdb=" CB CYS A2927 " pdb=" SG CYS A2927 " pdb=" SG CYS A2945 " pdb=" CB CYS A2945 " ideal model delta sinusoidal sigma weight residual -86.00 -169.42 83.42 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS A3701 " pdb=" SG CYS A3701 " pdb=" SG CYS A3716 " pdb=" CB CYS A3716 " ideal model delta sinusoidal sigma weight residual 93.00 166.24 -73.24 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS A3534 " pdb=" SG CYS A3534 " pdb=" SG CYS A3550 " pdb=" CB CYS A3550 " ideal model delta sinusoidal sigma weight residual 93.00 162.47 -69.47 1 1.00e+01 1.00e-02 6.23e+01 ... (remaining 7935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1329 0.050 - 0.100: 378 0.100 - 0.150: 82 0.150 - 0.200: 7 0.200 - 0.251: 4 Chirality restraints: 1800 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O3 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.72e+01 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE B4168 " pdb=" CA ILE B4168 " pdb=" CG1 ILE B4168 " pdb=" CG2 ILE B4168 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1797 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A4702 " -0.291 2.00e-02 2.50e+03 2.46e-01 7.58e+02 pdb=" C7 NAG A4702 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A4702 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG A4702 " 0.424 2.00e-02 2.50e+03 pdb=" O7 NAG A4702 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.202 2.00e-02 2.50e+03 1.69e-01 3.55e+02 pdb=" C7 NAG I 1 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.278 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.188 2.00e-02 2.50e+03 1.55e-01 3.02e+02 pdb=" C7 NAG G 1 " 0.049 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.253 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.022 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 520 2.70 - 3.25: 12431 3.25 - 3.80: 18496 3.80 - 4.35: 24081 4.35 - 4.90: 39236 Nonbonded interactions: 94764 Sorted by model distance: nonbonded pdb=" OD2 ASP A3585 " pdb="CA CA A4719 " model vdw 2.152 2.510 nonbonded pdb=" OD1 ASN A3575 " pdb="CA CA A4719 " model vdw 2.153 2.510 nonbonded pdb=" OD2 ASP A3025 " pdb="CA CA A4711 " model vdw 2.165 2.510 nonbonded pdb=" OD1 ASP A3015 " pdb="CA CA A4711 " model vdw 2.170 2.510 nonbonded pdb=" OE1 GLU A3713 " pdb="CA CA A4722 " model vdw 2.187 2.510 ... (remaining 94759 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 'C' selection = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' } 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 group one per residue 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: 1.450 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.140 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 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 : 0.005 0.141 12248 Z= 0.298 Angle : 0.800 9.710 16693 Z= 0.426 Chirality : 0.049 0.251 1800 Planarity : 0.010 0.246 2167 Dihedral : 18.364 108.880 5056 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.89 % Favored : 91.90 % Rotamer: Outliers : 2.95 % Allowed : 17.57 % Favored : 79.47 % 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: -1.12 (0.22), residues: 1432 helix: -2.94 (0.89), residues: 21 sheet: -1.38 (0.31), residues: 283 loop : -0.52 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B4176 TYR 0.013 0.001 TYR A3221 PHE 0.032 0.002 PHE A3891 TRP 0.010 0.001 TRP A3288 HIS 0.004 0.001 HIS A3451 Details of bonding type rmsd covalent geometry : bond 0.00478 (12149) covalent geometry : angle 0.79334 (16475) SS BOND : bond 0.00220 ( 64) SS BOND : angle 0.92532 ( 128) hydrogen bonds : bond 0.26108 ( 232) hydrogen bonds : angle 10.84627 ( 507) Misc. bond : bond 0.08402 ( 5) link_ALPHA1-3 : bond 0.00200 ( 3) link_ALPHA1-3 : angle 0.83551 ( 9) link_ALPHA1-6 : bond 0.00291 ( 3) link_ALPHA1-6 : angle 0.67795 ( 9) link_BETA1-3 : bond 0.00031 ( 1) link_BETA1-3 : angle 0.37067 ( 3) link_BETA1-4 : bond 0.00501 ( 14) link_BETA1-4 : angle 1.39490 ( 42) link_NAG-ASN : bond 0.00224 ( 9) link_NAG-ASN : angle 2.11694 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 58 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3622 LEU cc_start: 0.8741 (tp) cc_final: 0.8443 (mt) outliers start: 38 outliers final: 24 residues processed: 96 average time/residue: 0.0876 time to fit residues: 12.7017 Evaluate side-chains 80 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 2931 ASN Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3111 CYS Chi-restraints excluded: chain A residue 3165 CYS Chi-restraints excluded: chain A residue 3299 SER Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3416 THR Chi-restraints excluded: chain A residue 3468 SER Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3541 SER Chi-restraints excluded: chain A residue 3600 GLU Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3664 ASP Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3691 ASN Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain B residue 4192 ILE Chi-restraints excluded: chain B residue 4194 VAL Chi-restraints excluded: chain B residue 4311 LEU Chi-restraints excluded: chain B residue 4313 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2906 ASN A2931 ASN A2943 HIS A3262 ASN A3679 ASN A3714 GLN A3782 GLN B4145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.179834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.156630 restraints weight = 23272.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156306 restraints weight = 55910.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.155371 restraints weight = 19730.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.156010 restraints weight = 11930.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155762 restraints weight = 8905.472| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12248 Z= 0.145 Angle : 0.669 10.073 16693 Z= 0.337 Chirality : 0.047 0.195 1800 Planarity : 0.004 0.052 2167 Dihedral : 11.891 84.034 2356 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 3.27 % Allowed : 18.20 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.22), residues: 1432 helix: -2.46 (0.96), residues: 21 sheet: -1.01 (0.31), residues: 282 loop : -0.57 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B4176 TYR 0.020 0.002 TYR B4287 PHE 0.022 0.002 PHE A3205 TRP 0.010 0.001 TRP A3288 HIS 0.006 0.001 HIS A3312 Details of bonding type rmsd covalent geometry : bond 0.00332 (12149) covalent geometry : angle 0.64749 (16475) SS BOND : bond 0.00317 ( 64) SS BOND : angle 1.04903 ( 128) hydrogen bonds : bond 0.04347 ( 232) hydrogen bonds : angle 7.68457 ( 507) Misc. bond : bond 0.00142 ( 5) link_ALPHA1-3 : bond 0.00812 ( 3) link_ALPHA1-3 : angle 2.04298 ( 9) link_ALPHA1-6 : bond 0.00797 ( 3) link_ALPHA1-6 : angle 1.45077 ( 9) link_BETA1-3 : bond 0.00421 ( 1) link_BETA1-3 : angle 3.47416 ( 3) link_BETA1-4 : bond 0.00611 ( 14) link_BETA1-4 : angle 1.97872 ( 42) link_NAG-ASN : bond 0.00376 ( 9) link_NAG-ASN : angle 2.52154 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 62 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3204 ILE cc_start: 0.9112 (mt) cc_final: 0.8871 (pt) REVERT: A 3262 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8148 (t0) REVERT: A 3439 ASP cc_start: 0.8970 (p0) cc_final: 0.8394 (p0) REVERT: A 3590 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6583 (mp) REVERT: A 3737 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8625 (tt) REVERT: B 4145 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7380 (pm20) outliers start: 42 outliers final: 18 residues processed: 97 average time/residue: 0.0949 time to fit residues: 13.9565 Evaluate side-chains 81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2931 ASN Chi-restraints excluded: chain A residue 2955 PHE Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3111 CYS Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3262 ASN Chi-restraints excluded: chain A residue 3314 VAL Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3416 THR Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4145 GLN Chi-restraints excluded: chain B residue 4169 GLU Chi-restraints excluded: chain B residue 4170 VAL Chi-restraints excluded: chain B residue 4192 ILE Chi-restraints excluded: chain B residue 4414 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 63 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 114 optimal weight: 50.0000 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.180677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157550 restraints weight = 23456.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.157198 restraints weight = 56647.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156424 restraints weight = 19822.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157069 restraints weight = 12219.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156830 restraints weight = 8870.828| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12248 Z= 0.110 Angle : 0.636 14.900 16693 Z= 0.320 Chirality : 0.047 0.258 1800 Planarity : 0.004 0.052 2167 Dihedral : 9.966 77.018 2333 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.68 % Favored : 92.25 % Rotamer: Outliers : 3.19 % Allowed : 18.66 % Favored : 78.15 % 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: -0.99 (0.22), residues: 1432 helix: -2.44 (0.96), residues: 21 sheet: -0.98 (0.31), residues: 284 loop : -0.53 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4176 TYR 0.016 0.001 TYR B4287 PHE 0.022 0.001 PHE A3322 TRP 0.008 0.001 TRP A3288 HIS 0.003 0.000 HIS A3451 Details of bonding type rmsd covalent geometry : bond 0.00247 (12149) covalent geometry : angle 0.61315 (16475) SS BOND : bond 0.00259 ( 64) SS BOND : angle 1.25643 ( 128) hydrogen bonds : bond 0.03662 ( 232) hydrogen bonds : angle 7.14899 ( 507) Misc. bond : bond 0.00031 ( 5) link_ALPHA1-3 : bond 0.00928 ( 3) link_ALPHA1-3 : angle 1.55688 ( 9) link_ALPHA1-6 : bond 0.00725 ( 3) link_ALPHA1-6 : angle 1.61380 ( 9) link_BETA1-3 : bond 0.00551 ( 1) link_BETA1-3 : angle 2.81642 ( 3) link_BETA1-4 : bond 0.00493 ( 14) link_BETA1-4 : angle 1.90138 ( 42) link_NAG-ASN : bond 0.00192 ( 9) link_NAG-ASN : angle 2.23444 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.5156 (OUTLIER) cc_final: 0.4389 (p90) REVERT: A 3204 ILE cc_start: 0.9127 (mt) cc_final: 0.8884 (pt) REVERT: A 3439 ASP cc_start: 0.8935 (p0) cc_final: 0.8344 (p0) REVERT: A 3590 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6673 (mp) REVERT: A 3664 ASP cc_start: 0.7116 (m-30) cc_final: 0.6684 (t0) REVERT: A 3737 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8624 (tt) outliers start: 41 outliers final: 18 residues processed: 98 average time/residue: 0.0763 time to fit residues: 11.2941 Evaluate side-chains 81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2931 ASN Chi-restraints excluded: chain A residue 2972 TRP Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3178 CYS Chi-restraints excluded: chain A residue 3416 THR Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3597 GLU Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4192 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3903 GLN ** B4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.177793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154128 restraints weight = 23587.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.154003 restraints weight = 55837.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152441 restraints weight = 19792.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152606 restraints weight = 16016.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.152663 restraints weight = 9935.915| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12248 Z= 0.232 Angle : 0.714 14.184 16693 Z= 0.360 Chirality : 0.050 0.279 1800 Planarity : 0.005 0.050 2167 Dihedral : 9.539 72.878 2331 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.15 % Favored : 90.78 % Rotamer: Outliers : 3.50 % Allowed : 18.35 % Favored : 78.15 % 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: -1.15 (0.22), residues: 1432 helix: -2.22 (0.99), residues: 21 sheet: -1.03 (0.31), residues: 285 loop : -0.68 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B4176 TYR 0.017 0.002 TYR A3136 PHE 0.024 0.002 PHE A3205 TRP 0.009 0.001 TRP A3288 HIS 0.005 0.001 HIS A3451 Details of bonding type rmsd covalent geometry : bond 0.00542 (12149) covalent geometry : angle 0.68949 (16475) SS BOND : bond 0.00376 ( 64) SS BOND : angle 1.49814 ( 128) hydrogen bonds : bond 0.03692 ( 232) hydrogen bonds : angle 7.05499 ( 507) Misc. bond : bond 0.00089 ( 5) link_ALPHA1-3 : bond 0.00911 ( 3) link_ALPHA1-3 : angle 1.77912 ( 9) link_ALPHA1-6 : bond 0.00818 ( 3) link_ALPHA1-6 : angle 1.82945 ( 9) link_BETA1-3 : bond 0.00681 ( 1) link_BETA1-3 : angle 2.50290 ( 3) link_BETA1-4 : bond 0.00586 ( 14) link_BETA1-4 : angle 1.83227 ( 42) link_NAG-ASN : bond 0.00470 ( 9) link_NAG-ASN : angle 2.51217 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 59 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.5278 (OUTLIER) cc_final: 0.4660 (p90) REVERT: A 3204 ILE cc_start: 0.9239 (mt) cc_final: 0.8962 (pt) REVERT: A 3439 ASP cc_start: 0.8929 (p0) cc_final: 0.8357 (p0) REVERT: A 3590 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6881 (mp) REVERT: A 3737 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8817 (tt) REVERT: A 3843 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7505 (m-10) REVERT: A 3854 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7778 (m-70) REVERT: B 4188 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7548 (mm-40) outliers start: 45 outliers final: 29 residues processed: 97 average time/residue: 0.0784 time to fit residues: 11.6545 Evaluate side-chains 92 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 2931 ASN Chi-restraints excluded: chain A residue 2955 PHE Chi-restraints excluded: chain A residue 2972 TRP Chi-restraints excluded: chain A residue 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3039 PHE Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3178 CYS Chi-restraints excluded: chain A residue 3222 SER Chi-restraints excluded: chain A residue 3416 THR Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3513 MET Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3657 ASP Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain A residue 3843 TYR Chi-restraints excluded: chain A residue 3854 HIS Chi-restraints excluded: chain A residue 3855 VAL Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4188 GLN Chi-restraints excluded: chain B residue 4192 ILE Chi-restraints excluded: chain B residue 4414 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 16 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 136 optimal weight: 50.0000 chunk 133 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3262 ASN ** B4234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.154671 restraints weight = 23390.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154690 restraints weight = 55855.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.154167 restraints weight = 19144.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154870 restraints weight = 12312.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.154038 restraints weight = 9016.017| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12248 Z= 0.190 Angle : 0.675 12.347 16693 Z= 0.342 Chirality : 0.048 0.259 1800 Planarity : 0.004 0.051 2167 Dihedral : 9.034 68.802 2331 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.80 % Favored : 91.13 % Rotamer: Outliers : 4.04 % Allowed : 18.74 % Favored : 77.22 % 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: -1.12 (0.22), residues: 1432 helix: -2.09 (1.04), residues: 21 sheet: -1.10 (0.31), residues: 294 loop : -0.62 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3094 TYR 0.015 0.002 TYR A3136 PHE 0.025 0.002 PHE A3205 TRP 0.010 0.001 TRP A3288 HIS 0.005 0.001 HIS A3451 Details of bonding type rmsd covalent geometry : bond 0.00443 (12149) covalent geometry : angle 0.64983 (16475) SS BOND : bond 0.00327 ( 64) SS BOND : angle 1.45451 ( 128) hydrogen bonds : bond 0.03404 ( 232) hydrogen bonds : angle 6.83423 ( 507) Misc. bond : bond 0.00067 ( 5) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 1.77830 ( 9) link_ALPHA1-6 : bond 0.00788 ( 3) link_ALPHA1-6 : angle 1.85412 ( 9) link_BETA1-3 : bond 0.00530 ( 1) link_BETA1-3 : angle 2.08528 ( 3) link_BETA1-4 : bond 0.00545 ( 14) link_BETA1-4 : angle 1.76298 ( 42) link_NAG-ASN : bond 0.00325 ( 9) link_NAG-ASN : angle 2.51000 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 59 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.5190 (OUTLIER) cc_final: 0.4645 (p90) REVERT: A 3204 ILE cc_start: 0.9222 (mt) cc_final: 0.8966 (pt) REVERT: A 3262 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8142 (t0) REVERT: A 3439 ASP cc_start: 0.8944 (p0) cc_final: 0.8344 (p0) REVERT: A 3590 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6772 (mp) REVERT: A 3737 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8843 (tt) REVERT: B 4188 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7596 (mm-40) outliers start: 52 outliers final: 29 residues processed: 106 average time/residue: 0.0841 time to fit residues: 13.5149 Evaluate side-chains 92 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 2931 ASN Chi-restraints excluded: chain A residue 2955 PHE Chi-restraints excluded: chain A residue 2972 TRP Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3039 PHE Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3152 CYS Chi-restraints excluded: chain A residue 3178 CYS Chi-restraints excluded: chain A residue 3222 SER Chi-restraints excluded: chain A residue 3262 ASN Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3416 THR Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3502 VAL Chi-restraints excluded: chain A residue 3513 MET Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3707 CYS Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4188 GLN Chi-restraints excluded: chain B residue 4192 ILE Chi-restraints excluded: chain B residue 4414 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 128 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.179063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155417 restraints weight = 23295.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155489 restraints weight = 56134.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.154482 restraints weight = 19763.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.155295 restraints weight = 12094.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.154786 restraints weight = 8836.241| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12248 Z= 0.134 Angle : 0.651 15.182 16693 Z= 0.328 Chirality : 0.047 0.293 1800 Planarity : 0.004 0.051 2167 Dihedral : 8.417 62.616 2331 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.17 % Favored : 91.76 % Rotamer: Outliers : 3.34 % Allowed : 19.13 % Favored : 77.53 % 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: -1.03 (0.22), residues: 1432 helix: -2.05 (1.05), residues: 21 sheet: -0.97 (0.32), residues: 277 loop : -0.60 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3263 TYR 0.014 0.001 TYR A3221 PHE 0.022 0.001 PHE A3205 TRP 0.010 0.001 TRP A3288 HIS 0.004 0.001 HIS A3312 Details of bonding type rmsd covalent geometry : bond 0.00310 (12149) covalent geometry : angle 0.62319 (16475) SS BOND : bond 0.00321 ( 64) SS BOND : angle 1.60178 ( 128) hydrogen bonds : bond 0.03105 ( 232) hydrogen bonds : angle 6.60929 ( 507) Misc. bond : bond 0.00038 ( 5) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 1.78006 ( 9) link_ALPHA1-6 : bond 0.00790 ( 3) link_ALPHA1-6 : angle 1.84817 ( 9) link_BETA1-3 : bond 0.00507 ( 1) link_BETA1-3 : angle 1.94304 ( 3) link_BETA1-4 : bond 0.00502 ( 14) link_BETA1-4 : angle 1.68983 ( 42) link_NAG-ASN : bond 0.00288 ( 9) link_NAG-ASN : angle 2.36694 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 65 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.5109 (OUTLIER) cc_final: 0.4608 (p90) REVERT: A 3204 ILE cc_start: 0.9150 (mt) cc_final: 0.8875 (pt) REVERT: A 3439 ASP cc_start: 0.8886 (p0) cc_final: 0.8350 (p0) REVERT: A 3590 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6767 (mp) REVERT: A 3737 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8791 (tt) REVERT: B 4188 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7511 (mm-40) outliers start: 43 outliers final: 27 residues processed: 101 average time/residue: 0.0868 time to fit residues: 13.0107 Evaluate side-chains 95 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 2955 PHE Chi-restraints excluded: chain A residue 2972 TRP Chi-restraints excluded: chain A residue 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3178 CYS Chi-restraints excluded: chain A residue 3222 SER Chi-restraints excluded: chain A residue 3292 ILE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3657 ASP Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3684 THR Chi-restraints excluded: chain A residue 3707 CYS Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain A residue 3856 CYS Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4188 GLN Chi-restraints excluded: chain B residue 4192 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 117 optimal weight: 0.0980 chunk 80 optimal weight: 0.0470 chunk 133 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3614 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 = 0.4343 r_free = 0.4343 target = 0.180841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.157129 restraints weight = 23615.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.157717 restraints weight = 53258.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156945 restraints weight = 17171.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157087 restraints weight = 14074.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157254 restraints weight = 8638.439| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12248 Z= 0.121 Angle : 0.634 13.094 16693 Z= 0.320 Chirality : 0.047 0.266 1800 Planarity : 0.004 0.051 2167 Dihedral : 7.829 59.598 2328 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.75 % Favored : 92.18 % Rotamer: Outliers : 3.27 % Allowed : 19.75 % Favored : 76.98 % 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: -0.94 (0.23), residues: 1432 helix: -2.10 (1.04), residues: 21 sheet: -0.89 (0.32), residues: 285 loop : -0.52 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3123 TYR 0.014 0.001 TYR A3221 PHE 0.022 0.001 PHE A3205 TRP 0.010 0.001 TRP A3288 HIS 0.003 0.001 HIS A3451 Details of bonding type rmsd covalent geometry : bond 0.00276 (12149) covalent geometry : angle 0.60794 (16475) SS BOND : bond 0.00236 ( 64) SS BOND : angle 1.56972 ( 128) hydrogen bonds : bond 0.02969 ( 232) hydrogen bonds : angle 6.44344 ( 507) Misc. bond : bond 0.00027 ( 5) link_ALPHA1-3 : bond 0.01033 ( 3) link_ALPHA1-3 : angle 1.80222 ( 9) link_ALPHA1-6 : bond 0.00824 ( 3) link_ALPHA1-6 : angle 1.80753 ( 9) link_BETA1-3 : bond 0.00512 ( 1) link_BETA1-3 : angle 1.87340 ( 3) link_BETA1-4 : bond 0.00496 ( 14) link_BETA1-4 : angle 1.62267 ( 42) link_NAG-ASN : bond 0.00228 ( 9) link_NAG-ASN : angle 2.20659 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 64 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.4981 (OUTLIER) cc_final: 0.4643 (p90) REVERT: A 3026 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5024 (mt-10) REVERT: A 3204 ILE cc_start: 0.9138 (mt) cc_final: 0.8875 (pt) REVERT: A 3439 ASP cc_start: 0.8857 (p0) cc_final: 0.8370 (p0) REVERT: A 3590 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6714 (mp) REVERT: A 3664 ASP cc_start: 0.7025 (m-30) cc_final: 0.6481 (t0) REVERT: A 3737 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8769 (tt) REVERT: B 4188 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7495 (mm-40) outliers start: 42 outliers final: 28 residues processed: 97 average time/residue: 0.1008 time to fit residues: 14.3939 Evaluate side-chains 95 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 2955 PHE Chi-restraints excluded: chain A residue 2972 TRP Chi-restraints excluded: chain A residue 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3026 GLU Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3132 ILE Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3152 CYS Chi-restraints excluded: chain A residue 3178 CYS Chi-restraints excluded: chain A residue 3222 SER Chi-restraints excluded: chain A residue 3270 ARG Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3657 ASP Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3707 CYS Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain A residue 3856 CYS Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4170 VAL Chi-restraints excluded: chain B residue 4188 GLN Chi-restraints excluded: chain B residue 4192 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3614 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 = 0.4343 r_free = 0.4343 target = 0.180905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.157575 restraints weight = 23534.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.157762 restraints weight = 53832.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156295 restraints weight = 18244.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156562 restraints weight = 14385.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156622 restraints weight = 9192.790| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12248 Z= 0.124 Angle : 0.629 11.770 16693 Z= 0.318 Chirality : 0.046 0.232 1800 Planarity : 0.004 0.051 2167 Dihedral : 7.213 59.331 2328 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 3.19 % Allowed : 19.67 % Favored : 77.14 % 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: -0.93 (0.23), residues: 1432 helix: -2.11 (1.06), residues: 21 sheet: -0.83 (0.32), residues: 269 loop : -0.54 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3006 TYR 0.014 0.001 TYR A3221 PHE 0.022 0.001 PHE A3205 TRP 0.010 0.001 TRP B4288 HIS 0.003 0.001 HIS A3312 Details of bonding type rmsd covalent geometry : bond 0.00286 (12149) covalent geometry : angle 0.60553 (16475) SS BOND : bond 0.00228 ( 64) SS BOND : angle 1.44742 ( 128) hydrogen bonds : bond 0.02895 ( 232) hydrogen bonds : angle 6.29313 ( 507) Misc. bond : bond 0.00033 ( 5) link_ALPHA1-3 : bond 0.00991 ( 3) link_ALPHA1-3 : angle 1.75934 ( 9) link_ALPHA1-6 : bond 0.00789 ( 3) link_ALPHA1-6 : angle 1.80502 ( 9) link_BETA1-3 : bond 0.00511 ( 1) link_BETA1-3 : angle 1.81988 ( 3) link_BETA1-4 : bond 0.00519 ( 14) link_BETA1-4 : angle 1.58073 ( 42) link_NAG-ASN : bond 0.00254 ( 9) link_NAG-ASN : angle 2.11800 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 66 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.4991 (OUTLIER) cc_final: 0.4714 (p90) REVERT: A 3204 ILE cc_start: 0.9141 (mt) cc_final: 0.8884 (pt) REVERT: A 3439 ASP cc_start: 0.8873 (p0) cc_final: 0.8434 (p0) REVERT: A 3590 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6730 (mp) REVERT: A 3664 ASP cc_start: 0.7132 (m-30) cc_final: 0.6777 (t0) REVERT: A 3737 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8756 (tt) REVERT: B 4188 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7396 (mm-40) outliers start: 41 outliers final: 29 residues processed: 99 average time/residue: 0.0905 time to fit residues: 13.4256 Evaluate side-chains 95 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 2955 PHE Chi-restraints excluded: chain A residue 2972 TRP Chi-restraints excluded: chain A residue 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3152 CYS Chi-restraints excluded: chain A residue 3178 CYS Chi-restraints excluded: chain A residue 3222 SER Chi-restraints excluded: chain A residue 3270 ARG Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3502 VAL Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3657 ASP Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3707 CYS Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3757 VAL Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain A residue 3856 CYS Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4170 VAL Chi-restraints excluded: chain B residue 4180 TRP Chi-restraints excluded: chain B residue 4188 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 94 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 127 optimal weight: 30.0000 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 52 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3614 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 = 0.4351 r_free = 0.4351 target = 0.181486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.158046 restraints weight = 23539.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.158408 restraints weight = 52961.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156934 restraints weight = 17795.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.157162 restraints weight = 15030.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157272 restraints weight = 9937.374| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12248 Z= 0.116 Angle : 0.613 10.883 16693 Z= 0.309 Chirality : 0.046 0.200 1800 Planarity : 0.004 0.051 2167 Dihedral : 6.569 58.969 2326 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.61 % Favored : 92.32 % Rotamer: Outliers : 3.19 % Allowed : 19.83 % Favored : 76.98 % 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: -0.86 (0.23), residues: 1432 helix: -1.95 (1.10), residues: 20 sheet: -0.76 (0.32), residues: 281 loop : -0.49 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3006 TYR 0.013 0.001 TYR A3221 PHE 0.025 0.001 PHE A3413 TRP 0.011 0.001 TRP B4180 HIS 0.003 0.001 HIS A3451 Details of bonding type rmsd covalent geometry : bond 0.00267 (12149) covalent geometry : angle 0.59042 (16475) SS BOND : bond 0.00241 ( 64) SS BOND : angle 1.37351 ( 128) hydrogen bonds : bond 0.02814 ( 232) hydrogen bonds : angle 6.17865 ( 507) Misc. bond : bond 0.00032 ( 5) link_ALPHA1-3 : bond 0.01023 ( 3) link_ALPHA1-3 : angle 1.58507 ( 9) link_ALPHA1-6 : bond 0.00819 ( 3) link_ALPHA1-6 : angle 2.10064 ( 9) link_BETA1-3 : bond 0.00510 ( 1) link_BETA1-3 : angle 1.78573 ( 3) link_BETA1-4 : bond 0.00479 ( 14) link_BETA1-4 : angle 1.50950 ( 42) link_NAG-ASN : bond 0.00308 ( 9) link_NAG-ASN : angle 2.06101 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 67 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.4984 (OUTLIER) cc_final: 0.4726 (p90) REVERT: A 3204 ILE cc_start: 0.9136 (mt) cc_final: 0.8881 (pt) REVERT: A 3439 ASP cc_start: 0.8868 (p0) cc_final: 0.8445 (p0) REVERT: A 3590 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6780 (mp) REVERT: A 3600 GLU cc_start: 0.6239 (mp0) cc_final: 0.5234 (mt-10) REVERT: A 3664 ASP cc_start: 0.7106 (m-30) cc_final: 0.6778 (t0) REVERT: A 3737 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8743 (tt) outliers start: 41 outliers final: 32 residues processed: 100 average time/residue: 0.0931 time to fit residues: 13.9632 Evaluate side-chains 100 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 2955 PHE Chi-restraints excluded: chain A residue 2972 TRP Chi-restraints excluded: chain A residue 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3132 ILE Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3152 CYS Chi-restraints excluded: chain A residue 3178 CYS Chi-restraints excluded: chain A residue 3222 SER Chi-restraints excluded: chain A residue 3270 ARG Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3502 VAL Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3657 ASP Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3707 CYS Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain A residue 3856 CYS Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4107 VAL Chi-restraints excluded: chain B residue 4170 VAL Chi-restraints excluded: chain B residue 4180 TRP Chi-restraints excluded: chain B residue 4192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 132 optimal weight: 40.0000 chunk 36 optimal weight: 0.0170 chunk 109 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3614 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 = 0.4350 r_free = 0.4350 target = 0.181380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157568 restraints weight = 23870.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.157901 restraints weight = 54454.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156580 restraints weight = 17828.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156944 restraints weight = 12916.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156768 restraints weight = 8662.623| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12248 Z= 0.131 Angle : 0.623 10.591 16693 Z= 0.314 Chirality : 0.046 0.196 1800 Planarity : 0.004 0.050 2167 Dihedral : 6.476 58.999 2325 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.90 % Rotamer: Outliers : 2.72 % Allowed : 20.22 % Favored : 77.06 % 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: -0.88 (0.23), residues: 1432 helix: -1.82 (1.11), residues: 20 sheet: -0.71 (0.32), residues: 281 loop : -0.53 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3006 TYR 0.013 0.001 TYR A3221 PHE 0.023 0.001 PHE A3413 TRP 0.011 0.001 TRP B4288 HIS 0.004 0.001 HIS A3451 Details of bonding type rmsd covalent geometry : bond 0.00307 (12149) covalent geometry : angle 0.60146 (16475) SS BOND : bond 0.00221 ( 64) SS BOND : angle 1.36060 ( 128) hydrogen bonds : bond 0.02912 ( 232) hydrogen bonds : angle 6.16619 ( 507) Misc. bond : bond 0.00037 ( 5) link_ALPHA1-3 : bond 0.01008 ( 3) link_ALPHA1-3 : angle 1.63066 ( 9) link_ALPHA1-6 : bond 0.00840 ( 3) link_ALPHA1-6 : angle 2.06978 ( 9) link_BETA1-3 : bond 0.00505 ( 1) link_BETA1-3 : angle 1.76334 ( 3) link_BETA1-4 : bond 0.00484 ( 14) link_BETA1-4 : angle 1.44992 ( 42) link_NAG-ASN : bond 0.00259 ( 9) link_NAG-ASN : angle 2.06501 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.4994 (OUTLIER) cc_final: 0.4743 (p90) REVERT: A 3204 ILE cc_start: 0.9139 (mt) cc_final: 0.8873 (pt) REVERT: A 3439 ASP cc_start: 0.8891 (p0) cc_final: 0.8458 (p0) REVERT: A 3590 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6790 (mp) REVERT: A 3664 ASP cc_start: 0.7167 (m-30) cc_final: 0.6831 (t0) REVERT: A 3737 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8753 (tt) outliers start: 35 outliers final: 30 residues processed: 94 average time/residue: 0.0979 time to fit residues: 13.8935 Evaluate side-chains 94 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ILE Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 2972 TRP Chi-restraints excluded: chain A residue 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3132 ILE Chi-restraints excluded: chain A residue 3145 LEU Chi-restraints excluded: chain A residue 3152 CYS Chi-restraints excluded: chain A residue 3178 CYS Chi-restraints excluded: chain A residue 3222 SER Chi-restraints excluded: chain A residue 3270 ARG Chi-restraints excluded: chain A residue 3373 THR Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3502 VAL Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3621 CYS Chi-restraints excluded: chain A residue 3644 CYS Chi-restraints excluded: chain A residue 3657 ASP Chi-restraints excluded: chain A residue 3666 SER Chi-restraints excluded: chain A residue 3707 CYS Chi-restraints excluded: chain A residue 3737 LEU Chi-restraints excluded: chain A residue 3741 CYS Chi-restraints excluded: chain A residue 3842 THR Chi-restraints excluded: chain A residue 3856 CYS Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4107 VAL Chi-restraints excluded: chain B residue 4170 VAL Chi-restraints excluded: chain B residue 4192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 138 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 108 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3614 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 = 0.4335 r_free = 0.4335 target = 0.180112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.157072 restraints weight = 23741.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.157204 restraints weight = 52643.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155677 restraints weight = 18133.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155838 restraints weight = 15701.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155906 restraints weight = 9665.725| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12248 Z= 0.170 Angle : 0.648 11.137 16693 Z= 0.327 Chirality : 0.047 0.204 1800 Planarity : 0.004 0.049 2167 Dihedral : 6.574 59.117 2325 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.90 % Rotamer: Outliers : 3.03 % Allowed : 20.14 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.23), residues: 1432 helix: -1.81 (1.10), residues: 20 sheet: -0.83 (0.31), residues: 295 loop : -0.53 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3006 TYR 0.014 0.001 TYR A3221 PHE 0.022 0.002 PHE A3205 TRP 0.011 0.001 TRP B4288 HIS 0.004 0.001 HIS A3451 Details of bonding type rmsd covalent geometry : bond 0.00400 (12149) covalent geometry : angle 0.62519 (16475) SS BOND : bond 0.00259 ( 64) SS BOND : angle 1.45179 ( 128) hydrogen bonds : bond 0.03012 ( 232) hydrogen bonds : angle 6.23095 ( 507) Misc. bond : bond 0.00052 ( 5) link_ALPHA1-3 : bond 0.00983 ( 3) link_ALPHA1-3 : angle 1.61688 ( 9) link_ALPHA1-6 : bond 0.00840 ( 3) link_ALPHA1-6 : angle 2.14709 ( 9) link_BETA1-3 : bond 0.00503 ( 1) link_BETA1-3 : angle 1.74278 ( 3) link_BETA1-4 : bond 0.00495 ( 14) link_BETA1-4 : angle 1.42801 ( 42) link_NAG-ASN : bond 0.00324 ( 9) link_NAG-ASN : angle 2.20161 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1441.71 seconds wall clock time: 25 minutes 46.75 seconds (1546.75 seconds total)