Starting phenix.real_space_refine on Mon Dec 30 03:51:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxa_36694/12_2024/8jxa_36694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxa_36694/12_2024/8jxa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxa_36694/12_2024/8jxa_36694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxa_36694/12_2024/8jxa_36694.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxa_36694/12_2024/8jxa_36694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxa_36694/12_2024/8jxa_36694.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.17, per 1000 atoms: 0.60 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: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.68 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: 6.13 Time building geometry restraints manager: 3.90 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: 2.050 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.520 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- 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 0.040 12149 Z= 0.302 Angle : 0.793 9.710 16475 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP A3288 HIS 0.004 0.001 HIS A3451 PHE 0.032 0.002 PHE A3891 TYR 0.013 0.001 TYR A3221 ARG 0.011 0.000 ARG B4176 *********************** 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 : 1.311 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: 0.2226 time to fit residues: 32.7338 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 : 1.131 ------------------------------------------------------------------------------- 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 120 optimal weight: 0.0970 chunk 108 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 50.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 A3679 ASN A3714 GLN A3782 GLN B4145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12149 Z= 0.194 Angle : 0.638 10.691 16475 Z= 0.328 Chirality : 0.047 0.185 1800 Planarity : 0.004 0.052 2167 Dihedral : 11.995 84.375 2356 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.12 % Favored : 92.81 % Rotamer: Outliers : 2.95 % Allowed : 18.12 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1432 helix: -2.50 (0.95), residues: 21 sheet: -0.99 (0.31), residues: 282 loop : -0.55 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3288 HIS 0.006 0.001 HIS A3312 PHE 0.022 0.001 PHE A3205 TYR 0.019 0.002 TYR B4287 ARG 0.006 0.000 ARG B4176 *********************** 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 100 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3204 ILE cc_start: 0.9135 (mt) cc_final: 0.8905 (pt) REVERT: A 3439 ASP cc_start: 0.9090 (p0) cc_final: 0.8543 (p0) REVERT: A 3513 MET cc_start: 0.8127 (tmm) cc_final: 0.7803 (tmm) REVERT: A 3590 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6735 (mp) REVERT: A 3622 LEU cc_start: 0.8656 (tp) cc_final: 0.8389 (mt) REVERT: A 3737 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 3891 PHE cc_start: 0.6611 (t80) cc_final: 0.6396 (t80) REVERT: B 4145 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6299 (pm20) REVERT: B 4179 LYS cc_start: 0.8912 (tmmt) cc_final: 0.8456 (tmmt) outliers start: 38 outliers final: 17 residues processed: 93 average time/residue: 0.2464 time to fit residues: 34.6200 Evaluate side-chains 78 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2931 ASN 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 3314 VAL 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 4313 VAL 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 72 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3262 ASN B4145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12149 Z= 0.305 Angle : 0.664 14.053 16475 Z= 0.340 Chirality : 0.049 0.285 1800 Planarity : 0.004 0.052 2167 Dihedral : 10.515 78.637 2333 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.55 % Rotamer: Outliers : 4.51 % Allowed : 17.65 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1432 helix: -2.37 (0.95), residues: 21 sheet: -1.06 (0.31), residues: 289 loop : -0.61 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3288 HIS 0.005 0.001 HIS A3451 PHE 0.027 0.002 PHE A3322 TYR 0.016 0.002 TYR B4287 ARG 0.005 0.000 ARG B4176 *********************** 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 117 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 59 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.4536 (OUTLIER) cc_final: 0.4240 (p90) REVERT: A 3071 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6874 (t70) REVERT: A 3204 ILE cc_start: 0.9232 (mt) cc_final: 0.8930 (pt) REVERT: A 3262 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8410 (t0) REVERT: A 3439 ASP cc_start: 0.9110 (p0) cc_final: 0.8605 (p0) REVERT: A 3498 ASP cc_start: 0.8136 (p0) cc_final: 0.7902 (p0) REVERT: A 3513 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7518 (tmm) REVERT: A 3590 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6673 (mp) REVERT: A 3622 LEU cc_start: 0.8638 (tp) cc_final: 0.8356 (mt) REVERT: A 3664 ASP cc_start: 0.7450 (m-30) cc_final: 0.7094 (t0) REVERT: A 3737 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8783 (tt) REVERT: A 3891 PHE cc_start: 0.6336 (t80) cc_final: 0.6121 (t80) REVERT: B 4145 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: B 4179 LYS cc_start: 0.8943 (tmmt) cc_final: 0.8691 (tmmt) outliers start: 58 outliers final: 22 residues processed: 105 average time/residue: 0.2299 time to fit residues: 37.2819 Evaluate side-chains 88 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 3052 VAL Chi-restraints excluded: chain A residue 3071 HIS 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 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 3513 MET Chi-restraints excluded: chain A residue 3590 LEU 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 3855 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 4192 ILE Chi-restraints excluded: chain B residue 4414 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 130 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 68 optimal weight: 0.0370 chunk 123 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4145 GLN B4234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12149 Z= 0.176 Angle : 0.618 13.705 16475 Z= 0.317 Chirality : 0.047 0.237 1800 Planarity : 0.004 0.056 2167 Dihedral : 9.121 71.358 2331 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 3.11 % Allowed : 18.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1432 helix: -2.31 (1.01), residues: 21 sheet: -0.96 (0.31), residues: 280 loop : -0.58 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A3288 HIS 0.003 0.001 HIS A3451 PHE 0.022 0.001 PHE A3205 TYR 0.016 0.001 TYR B4287 ARG 0.004 0.000 ARG B4176 *********************** 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 108 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2972 TRP cc_start: 0.4920 (OUTLIER) cc_final: 0.4697 (p90) REVERT: A 3071 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6688 (t70) REVERT: A 3204 ILE cc_start: 0.9184 (mt) cc_final: 0.8912 (pt) REVERT: A 3439 ASP cc_start: 0.9086 (p0) cc_final: 0.8588 (p0) REVERT: A 3513 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7802 (tmm) REVERT: A 3590 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6516 (mp) REVERT: A 3622 LEU cc_start: 0.8621 (tp) cc_final: 0.8339 (mt) REVERT: A 3664 ASP cc_start: 0.7511 (m-30) cc_final: 0.7044 (t0) REVERT: A 3737 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8747 (tt) REVERT: A 3891 PHE cc_start: 0.6677 (t80) cc_final: 0.6465 (t80) REVERT: B 4145 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6640 (pm20) REVERT: B 4179 LYS cc_start: 0.8962 (tmmt) cc_final: 0.8716 (tmmt) outliers start: 40 outliers final: 28 residues processed: 100 average time/residue: 0.2233 time to fit residues: 34.8134 Evaluate side-chains 97 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 3052 VAL Chi-restraints excluded: chain A residue 3071 HIS 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 3373 THR 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 3597 GLU 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 3843 TYR Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4144 MET Chi-restraints excluded: chain B residue 4145 GLN Chi-restraints excluded: chain B residue 4192 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 0.0370 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3262 ASN ** A3614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12149 Z= 0.183 Angle : 0.602 11.928 16475 Z= 0.308 Chirality : 0.046 0.225 1800 Planarity : 0.004 0.051 2167 Dihedral : 8.396 65.572 2331 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 3.50 % Allowed : 19.05 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1432 helix: -2.26 (1.01), residues: 21 sheet: -0.95 (0.31), residues: 287 loop : -0.50 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A3288 HIS 0.003 0.001 HIS A3451 PHE 0.022 0.001 PHE A3205 TYR 0.015 0.001 TYR B4287 ARG 0.003 0.000 ARG B4176 *********************** 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 110 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3071 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6862 (t70) REVERT: A 3204 ILE cc_start: 0.9164 (mt) cc_final: 0.8907 (pt) REVERT: A 3262 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.7923 (t0) REVERT: A 3439 ASP cc_start: 0.9084 (p0) cc_final: 0.8574 (p0) REVERT: A 3590 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6655 (mp) REVERT: A 3622 LEU cc_start: 0.8568 (tp) cc_final: 0.8294 (mt) REVERT: A 3664 ASP cc_start: 0.7549 (m-30) cc_final: 0.7058 (t0) REVERT: A 3737 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8741 (tt) REVERT: A 3854 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7939 (m-70) REVERT: A 3891 PHE cc_start: 0.6679 (t80) cc_final: 0.6469 (t80) REVERT: B 4145 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: B 4169 GLU cc_start: 0.6424 (mm-30) cc_final: 0.6088 (mm-30) REVERT: B 4179 LYS cc_start: 0.8943 (tmmt) cc_final: 0.8656 (tmmt) outliers start: 45 outliers final: 26 residues processed: 102 average time/residue: 0.2272 time to fit residues: 35.5234 Evaluate side-chains 96 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3071 HIS Chi-restraints excluded: chain A residue 3090 ILE Chi-restraints excluded: chain A residue 3145 LEU 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 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 3597 GLU 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 3854 HIS Chi-restraints excluded: chain A residue 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4144 MET Chi-restraints excluded: chain B residue 4145 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 46 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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** B4145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12149 Z= 0.179 Angle : 0.598 14.755 16475 Z= 0.307 Chirality : 0.047 0.287 1800 Planarity : 0.004 0.051 2167 Dihedral : 7.962 60.093 2328 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.75 % Favored : 92.18 % Rotamer: Outliers : 3.27 % Allowed : 19.44 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1432 helix: -2.12 (1.05), residues: 20 sheet: -0.91 (0.31), residues: 287 loop : -0.49 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B4288 HIS 0.003 0.001 HIS A3451 PHE 0.021 0.001 PHE A3205 TYR 0.014 0.001 TYR B4287 ARG 0.004 0.000 ARG A3123 *********************** 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: 42 poor density : 66 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3071 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6857 (t70) REVERT: A 3123 ARG cc_start: 0.7006 (mtt90) cc_final: 0.6720 (mpt180) REVERT: A 3204 ILE cc_start: 0.9160 (mt) cc_final: 0.8903 (pt) REVERT: A 3439 ASP cc_start: 0.9024 (p0) cc_final: 0.8584 (p0) REVERT: A 3590 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6653 (mp) REVERT: A 3622 LEU cc_start: 0.8569 (tp) cc_final: 0.8288 (mt) REVERT: A 3664 ASP cc_start: 0.7528 (m-30) cc_final: 0.7215 (t0) REVERT: A 3737 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8737 (tt) REVERT: A 3891 PHE cc_start: 0.6654 (t80) cc_final: 0.6451 (t80) REVERT: B 4145 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6604 (pm20) REVERT: B 4169 GLU cc_start: 0.6401 (mm-30) cc_final: 0.6047 (mm-30) REVERT: B 4179 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8671 (tmmt) outliers start: 42 outliers final: 30 residues processed: 98 average time/residue: 0.2396 time to fit residues: 35.6639 Evaluate side-chains 99 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3071 HIS 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 3373 THR 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 3597 GLU 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 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4107 VAL Chi-restraints excluded: chain B residue 4144 MET Chi-restraints excluded: chain B residue 4145 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 116 optimal weight: 0.0870 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 0.0670 chunk 85 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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** B4145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12149 Z= 0.167 Angle : 0.594 13.036 16475 Z= 0.303 Chirality : 0.046 0.258 1800 Planarity : 0.004 0.051 2167 Dihedral : 7.552 59.556 2328 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.54 % Favored : 92.39 % Rotamer: Outliers : 3.27 % Allowed : 19.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1432 helix: -2.09 (1.06), residues: 20 sheet: -0.78 (0.32), residues: 283 loop : -0.50 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2972 HIS 0.003 0.000 HIS A3451 PHE 0.021 0.001 PHE A3205 TYR 0.014 0.001 TYR B4287 ARG 0.004 0.000 ARG A3123 *********************** 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 108 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 66 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3071 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6857 (t70) REVERT: A 3123 ARG cc_start: 0.6960 (mtt90) cc_final: 0.6546 (mpt180) REVERT: A 3204 ILE cc_start: 0.9159 (mt) cc_final: 0.8903 (pt) REVERT: A 3439 ASP cc_start: 0.9021 (p0) cc_final: 0.8588 (p0) REVERT: A 3590 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6675 (mp) REVERT: A 3622 LEU cc_start: 0.8563 (tp) cc_final: 0.8284 (mt) REVERT: A 3664 ASP cc_start: 0.7530 (m-30) cc_final: 0.7236 (t0) REVERT: A 3737 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8724 (tt) REVERT: B 4145 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: B 4179 LYS cc_start: 0.8918 (tmmt) cc_final: 0.8686 (tmmt) outliers start: 42 outliers final: 30 residues processed: 99 average time/residue: 0.2800 time to fit residues: 40.3540 Evaluate side-chains 98 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3071 HIS 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 3373 THR 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 3597 GLU 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 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4107 VAL Chi-restraints excluded: chain B residue 4144 MET Chi-restraints excluded: chain B residue 4145 GLN Chi-restraints excluded: chain B residue 4170 VAL 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 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.0270 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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** A3733 HIS B4145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12149 Z= 0.165 Angle : 0.589 11.674 16475 Z= 0.301 Chirality : 0.046 0.228 1800 Planarity : 0.004 0.051 2167 Dihedral : 6.897 59.997 2328 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.61 % Favored : 92.32 % Rotamer: Outliers : 2.88 % Allowed : 19.52 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1432 helix: -2.03 (1.07), residues: 20 sheet: -0.72 (0.32), residues: 283 loop : -0.48 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B4288 HIS 0.003 0.000 HIS A3451 PHE 0.024 0.001 PHE A3413 TYR 0.014 0.001 TYR B4287 ARG 0.004 0.000 ARG B4176 *********************** 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 103 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3045 ARG cc_start: 0.6340 (ttt180) cc_final: 0.5934 (mtp180) REVERT: A 3071 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6856 (t70) REVERT: A 3123 ARG cc_start: 0.7069 (mtt90) cc_final: 0.6683 (mpt180) REVERT: A 3204 ILE cc_start: 0.9156 (mt) cc_final: 0.8904 (pt) REVERT: A 3439 ASP cc_start: 0.9036 (p0) cc_final: 0.8626 (p0) REVERT: A 3622 LEU cc_start: 0.8647 (tp) cc_final: 0.8297 (mt) REVERT: A 3664 ASP cc_start: 0.7529 (m-30) cc_final: 0.7238 (t0) REVERT: A 3737 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8651 (tt) REVERT: B 4145 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: B 4179 LYS cc_start: 0.8910 (tmmt) cc_final: 0.8680 (tmmt) outliers start: 37 outliers final: 28 residues processed: 94 average time/residue: 0.2551 time to fit residues: 35.7186 Evaluate side-chains 93 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 3009 ARG Chi-restraints excluded: chain A residue 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3071 HIS Chi-restraints excluded: chain A residue 3090 ILE 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 3478 CYS Chi-restraints excluded: chain A residue 3514 CYS Chi-restraints excluded: chain A residue 3562 CYS Chi-restraints excluded: chain A residue 3597 GLU 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 3881 PHE Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4107 VAL Chi-restraints excluded: chain B residue 4144 MET Chi-restraints excluded: chain B residue 4145 GLN Chi-restraints excluded: chain B residue 4170 VAL Chi-restraints excluded: chain B residue 4192 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 50.0000 chunk 120 optimal weight: 0.4980 chunk 128 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** A3903 GLN B4145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12149 Z= 0.245 Angle : 0.624 11.505 16475 Z= 0.319 Chirality : 0.047 0.216 1800 Planarity : 0.004 0.050 2167 Dihedral : 6.827 59.997 2327 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.61 % Favored : 92.32 % Rotamer: Outliers : 3.03 % Allowed : 19.52 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1432 helix: -1.92 (1.07), residues: 20 sheet: -0.80 (0.32), residues: 276 loop : -0.52 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2972 HIS 0.004 0.001 HIS A3451 PHE 0.021 0.002 PHE A3205 TYR 0.013 0.001 TYR A3221 ARG 0.005 0.000 ARG B4176 *********************** 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 101 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 62 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3071 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6867 (t70) REVERT: A 3123 ARG cc_start: 0.7199 (mtt90) cc_final: 0.6958 (mpt180) REVERT: A 3204 ILE cc_start: 0.9171 (mt) cc_final: 0.8903 (pt) REVERT: A 3439 ASP cc_start: 0.9043 (p0) cc_final: 0.8612 (p0) REVERT: A 3590 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6703 (mp) REVERT: A 3622 LEU cc_start: 0.8652 (tp) cc_final: 0.8296 (mt) REVERT: A 3664 ASP cc_start: 0.7524 (m-30) cc_final: 0.7210 (t0) REVERT: A 3737 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8769 (tt) REVERT: A 3903 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: B 4145 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6610 (pm20) outliers start: 39 outliers final: 27 residues processed: 94 average time/residue: 0.2623 time to fit residues: 36.9762 Evaluate side-chains 92 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3071 HIS 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 3373 THR 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 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 A residue 3903 GLN Chi-restraints excluded: chain B residue 4106 THR Chi-restraints excluded: chain B residue 4107 VAL Chi-restraints excluded: chain B residue 4144 MET Chi-restraints excluded: chain B residue 4145 GLN Chi-restraints excluded: chain B residue 4170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.8980 chunk 82 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 chunk 142 optimal weight: 50.0000 chunk 131 optimal weight: 30.0000 chunk 113 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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** B4145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12149 Z= 0.178 Angle : 0.605 11.035 16475 Z= 0.308 Chirality : 0.046 0.199 1800 Planarity : 0.004 0.051 2167 Dihedral : 6.460 59.608 2325 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.61 % Favored : 92.32 % Rotamer: Outliers : 2.80 % Allowed : 19.60 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1432 helix: -1.85 (1.10), residues: 20 sheet: -0.74 (0.32), residues: 284 loop : -0.48 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B4160 HIS 0.005 0.001 HIS A3902 PHE 0.021 0.001 PHE A3205 TYR 0.014 0.001 TYR A3221 ARG 0.005 0.000 ARG B4176 ********************** 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: 36 poor density : 64 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3071 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6860 (t70) REVERT: A 3123 ARG cc_start: 0.7171 (mtt90) cc_final: 0.6953 (mpt180) REVERT: A 3204 ILE cc_start: 0.9160 (mt) cc_final: 0.8895 (pt) REVERT: A 3439 ASP cc_start: 0.9038 (p0) cc_final: 0.8605 (p0) REVERT: A 3590 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6692 (mp) REVERT: A 3622 LEU cc_start: 0.8643 (tp) cc_final: 0.8284 (mt) REVERT: A 3664 ASP cc_start: 0.7595 (m-30) cc_final: 0.7289 (t0) REVERT: A 3737 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8743 (tt) REVERT: B 4145 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6721 (pm20) outliers start: 36 outliers final: 26 residues processed: 94 average time/residue: 0.2938 time to fit residues: 41.1314 Evaluate side-chains 93 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 3014 CYS Chi-restraints excluded: chain A residue 3052 VAL Chi-restraints excluded: chain A residue 3071 HIS Chi-restraints excluded: chain A residue 3090 ILE 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 3478 CYS 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 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 4145 GLN Chi-restraints excluded: chain B residue 4170 VAL Chi-restraints excluded: chain B residue 4287 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 116 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** B4145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.181564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.158207 restraints weight = 23334.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158480 restraints weight = 54863.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.157436 restraints weight = 18136.352| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12149 Z= 0.182 Angle : 0.598 9.619 16475 Z= 0.305 Chirality : 0.046 0.203 1800 Planarity : 0.004 0.051 2167 Dihedral : 6.322 59.853 2325 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer: Outliers : 2.64 % Allowed : 19.67 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1432 helix: -1.82 (1.10), residues: 20 sheet: -0.78 (0.32), residues: 288 loop : -0.46 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B4160 HIS 0.003 0.000 HIS A3451 PHE 0.021 0.001 PHE A3205 TYR 0.013 0.001 TYR A3221 ARG 0.005 0.000 ARG B4176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.23 seconds wall clock time: 40 minutes 53.62 seconds (2453.62 seconds total)