Starting phenix.real_space_refine on Wed Apr 30 18:34:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxf_36699/04_2025/8jxf_36699.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxf_36699/04_2025/8jxf_36699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxf_36699/04_2025/8jxf_36699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxf_36699/04_2025/8jxf_36699.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxf_36699/04_2025/8jxf_36699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxf_36699/04_2025/8jxf_36699.cif" } resolution = 3.6 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 134 5.16 5 C 5789 2.51 5 N 1686 2.21 5 O 1989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9618 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 599 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "B" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8548 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 53, 'TRANS': 1035} Chain breaks: 1 Chain: "O" 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: "A" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 104 Unusual residues: {' CA': 20, 'A2G': 4, 'NAG': 2} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.50, per 1000 atoms: 0.68 Number of scatterers: 9618 At special positions: 0 Unit cell: (91.715, 129.812, 146.744, 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 134 16.00 O 1989 8.00 N 1686 7.00 C 5789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=58, symmetry=0 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1244 " distance=2.03 Simple disulfide: pdb=" SG CYS B2865 " - pdb=" SG CYS B2878 " distance=2.03 Simple disulfide: pdb=" SG CYS B2872 " - pdb=" SG CYS B2891 " distance=2.03 Simple disulfide: pdb=" SG CYS B2885 " - pdb=" SG CYS B2901 " distance=2.03 Simple disulfide: pdb=" SG CYS B2908 " - pdb=" SG CYS B2920 " distance=2.03 Simple disulfide: pdb=" SG CYS B2915 " - pdb=" SG CYS B2933 " distance=2.03 Simple disulfide: pdb=" SG CYS B2927 " - pdb=" SG CYS B2945 " distance=2.03 Simple disulfide: pdb=" SG CYS B2950 " - pdb=" SG CYS B2967 " distance=2.03 Simple disulfide: pdb=" SG CYS B2957 " - pdb=" SG CYS B2980 " distance=2.03 Simple disulfide: pdb=" SG CYS B2974 " - pdb=" SG CYS B2990 " distance=2.03 Simple disulfide: pdb=" SG CYS B2995 " - pdb=" SG CYS B3007 " distance=2.03 Simple disulfide: pdb=" SG CYS B3002 " - pdb=" SG CYS B3020 " distance=2.04 Simple disulfide: pdb=" SG CYS B3014 " - pdb=" SG CYS B3029 " distance=2.03 Simple disulfide: pdb=" SG CYS B3034 " - pdb=" SG CYS B3046 " distance=2.03 Simple disulfide: pdb=" SG CYS B3041 " - pdb=" SG CYS B3059 " distance=2.03 Simple disulfide: pdb=" SG CYS B3053 " - pdb=" SG CYS B3070 " distance=2.03 Simple disulfide: pdb=" SG CYS B3077 " - pdb=" SG CYS B3089 " distance=2.03 Simple disulfide: pdb=" SG CYS B3084 " - pdb=" SG CYS B3102 " distance=2.03 Simple disulfide: pdb=" SG CYS B3096 " - pdb=" SG CYS B3111 " distance=2.03 Simple disulfide: pdb=" SG CYS B3116 " - pdb=" SG CYS B3128 " distance=2.03 Simple disulfide: pdb=" SG CYS B3124 " - pdb=" SG CYS B3137 " distance=2.03 Simple disulfide: pdb=" SG CYS B3139 " - pdb=" SG CYS B3152 " distance=2.03 Simple disulfide: pdb=" SG CYS B3158 " - pdb=" SG CYS B3169 " distance=2.03 Simple disulfide: pdb=" SG CYS B3165 " - pdb=" SG CYS B3178 " distance=2.03 Simple disulfide: pdb=" SG CYS B3180 " - pdb=" SG CYS B3193 " distance=2.03 Simple disulfide: pdb=" SG CYS B3313 " - pdb=" SG CYS B3321 " distance=2.03 Simple disulfide: pdb=" SG CYS B3471 " - pdb=" SG CYS B3482 " distance=2.03 Simple disulfide: pdb=" SG CYS B3478 " - pdb=" SG CYS B3493 " distance=2.03 Simple disulfide: pdb=" SG CYS B3495 " - pdb=" SG CYS B3510 " distance=2.03 Simple disulfide: pdb=" SG CYS B3514 " - pdb=" SG CYS B3527 " distance=2.03 Simple disulfide: pdb=" SG CYS B3521 " - pdb=" SG CYS B3540 " distance=2.03 Simple disulfide: pdb=" SG CYS B3534 " - pdb=" SG CYS B3550 " distance=2.03 Simple disulfide: pdb=" SG CYS B3555 " - pdb=" SG CYS B3567 " distance=2.03 Simple disulfide: pdb=" SG CYS B3562 " - pdb=" SG CYS B3580 " distance=2.03 Simple disulfide: pdb=" SG CYS B3574 " - pdb=" SG CYS B3591 " distance=2.03 Simple disulfide: pdb=" SG CYS B3596 " - pdb=" SG CYS B3608 " distance=2.03 Simple disulfide: pdb=" SG CYS B3603 " - pdb=" SG CYS B3621 " distance=2.03 Simple disulfide: pdb=" SG CYS B3615 " - pdb=" SG CYS B3632 " distance=2.03 Simple disulfide: pdb=" SG CYS B3644 " - pdb=" SG CYS B3662 " distance=2.03 Simple disulfide: pdb=" SG CYS B3656 " - pdb=" SG CYS B3673 " distance=2.03 Simple disulfide: pdb=" SG CYS B3680 " - pdb=" SG CYS B3694 " distance=2.03 Simple disulfide: pdb=" SG CYS B3688 " - pdb=" SG CYS B3707 " distance=2.03 Simple disulfide: pdb=" SG CYS B3701 " - pdb=" SG CYS B3716 " distance=2.03 Simple disulfide: pdb=" SG CYS B3721 " - pdb=" SG CYS B3734 " distance=2.03 Simple disulfide: pdb=" SG CYS B3729 " - pdb=" SG CYS B3747 " distance=2.03 Simple disulfide: pdb=" SG CYS B3741 " - pdb=" SG CYS B3756 " distance=2.03 Simple disulfide: pdb=" SG CYS B3761 " - pdb=" SG CYS B3773 " distance=2.03 Simple disulfide: pdb=" SG CYS B3768 " - pdb=" SG CYS B3786 " distance=2.03 Simple disulfide: pdb=" SG CYS B3780 " - pdb=" SG CYS B3795 " distance=2.03 Simple disulfide: pdb=" SG CYS B3800 " - pdb=" SG CYS B3812 " distance=2.03 Simple disulfide: pdb=" SG CYS B3807 " - pdb=" SG CYS B3825 " distance=2.03 Simple disulfide: pdb=" SG CYS B3819 " - pdb=" SG CYS B3834 " distance=2.03 Simple disulfide: pdb=" SG CYS B3844 " - pdb=" SG CYS B3856 " distance=2.03 Simple disulfide: pdb=" SG CYS B3851 " - pdb=" SG CYS B3869 " distance=2.03 Simple disulfide: pdb=" SG CYS B3863 " - pdb=" SG CYS B3880 " distance=2.03 Simple disulfide: pdb=" SG CYS B3885 " - pdb=" SG CYS B3898 " distance=2.03 Simple disulfide: pdb=" SG CYS B3893 " - pdb=" SG CYS B3911 " distance=2.03 Simple disulfide: pdb=" SG CYS B3905 " - pdb=" SG CYS B3922 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " BETA1-3 " NAG A 1 " - " NAG A 2 " " NAG D 2 " - " BMA D 3 " BETA1-4 " NAG A 2 " - " BMA A 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 1 " - " ASN B3127 " " NAG B4701 " - " ASN B3448 " " NAG B4702 " - " ASN B3682 " " NAG D 1 " - " ASN B3213 " " NAG E 1 " - " ASN B3259 " " NAG F 1 " - " ASN B3317 " " NAG G 1 " - " ASN B3357 " " NAG H 1 " - " ASN B3566 " " NAG I 1 " - " ASN B3840 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 28 sheets defined 17.6% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'C' and resid 59 through 73 removed outlier: 3.777A pdb=" N LYS C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 70 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 103 removed outlier: 3.588A pdb=" N ARG C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 125 removed outlier: 4.507A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 2922 through 2928 removed outlier: 3.835A pdb=" N VAL B2926 " --> pdb=" O GLY B2923 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B2927 " --> pdb=" O ASN B2924 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B2928 " --> pdb=" O TRP B2925 " (cutoff:3.500A) Processing helix chain 'B' and resid 2984 through 2988 removed outlier: 3.615A pdb=" N GLN B2988 " --> pdb=" O ASP B2985 " (cutoff:3.500A) Processing helix chain 'B' and resid 3011 through 3013 No H-bonds generated for 'chain 'B' and resid 3011 through 3013' Processing helix chain 'B' and resid 3023 through 3027 removed outlier: 3.521A pdb=" N ARG B3027 " --> pdb=" O SER B3024 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3052 No H-bonds generated for 'chain 'B' and resid 3050 through 3052' Processing helix chain 'B' and resid 3062 through 3066 removed outlier: 3.856A pdb=" N GLN B3066 " --> pdb=" O SER B3063 " (cutoff:3.500A) Processing helix chain 'B' and resid 3093 through 3095 No H-bonds generated for 'chain 'B' and resid 3093 through 3095' Processing helix chain 'B' and resid 3114 through 3119 Processing helix chain 'B' and resid 3156 through 3161 Processing helix chain 'B' and resid 3460 through 3464 removed outlier: 3.557A pdb=" N GLN B3464 " --> pdb=" O PRO B3461 " (cutoff:3.500A) Processing helix chain 'B' and resid 3473 through 3478 Processing helix chain 'B' and resid 3531 through 3533 No H-bonds generated for 'chain 'B' and resid 3531 through 3533' Processing helix chain 'B' and resid 3569 through 3573 Processing helix chain 'B' and resid 3583 through 3586 Processing helix chain 'B' and resid 3587 through 3592 Processing helix chain 'B' and resid 3612 through 3614 No H-bonds generated for 'chain 'B' and resid 3612 through 3614' Processing helix chain 'B' and resid 3628 through 3635 Processing helix chain 'B' and resid 3653 through 3655 No H-bonds generated for 'chain 'B' and resid 3653 through 3655' Processing helix chain 'B' and resid 3669 through 3674 Processing helix chain 'B' and resid 3675 through 3679 Processing helix chain 'B' and resid 3698 through 3700 No H-bonds generated for 'chain 'B' and resid 3698 through 3700' Processing helix chain 'B' and resid 3715 through 3719 removed outlier: 3.559A pdb=" N SER B3718 " --> pdb=" O GLY B3715 " (cutoff:3.500A) Processing helix chain 'B' and resid 3738 through 3740 No H-bonds generated for 'chain 'B' and resid 3738 through 3740' Processing helix chain 'B' and resid 3777 through 3779 No H-bonds generated for 'chain 'B' and resid 3777 through 3779' Processing helix chain 'B' and resid 3794 through 3798 Processing helix chain 'B' and resid 3816 through 3818 No H-bonds generated for 'chain 'B' and resid 3816 through 3818' Processing helix chain 'B' and resid 3858 through 3862 Processing helix chain 'B' and resid 3872 through 3876 removed outlier: 3.636A pdb=" N GLU B3876 " --> pdb=" O SER B3873 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3881 Processing helix chain 'B' and resid 3902 through 3904 No H-bonds generated for 'chain 'B' and resid 3902 through 3904' Processing helix chain 'B' and resid 3918 through 3922 Processing sheet with id=AA1, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id=AA2, first strand: chain 'B' and resid 2869 through 2871 Processing sheet with id=AA3, first strand: chain 'B' and resid 2914 through 2916 Processing sheet with id=AA4, first strand: chain 'B' and resid 2954 through 2955 Processing sheet with id=AA5, first strand: chain 'B' and resid 2999 through 3001 Processing sheet with id=AA6, first strand: chain 'B' and resid 3038 through 3039 Processing sheet with id=AA7, first strand: chain 'B' and resid 3081 through 3083 Processing sheet with id=AA8, first strand: chain 'B' and resid 3128 through 3130 Processing sheet with id=AA9, first strand: chain 'B' and resid 3143 through 3145 Processing sheet with id=AB1, first strand: chain 'B' and resid 3169 through 3172 Processing sheet with id=AB2, first strand: chain 'B' and resid 3184 through 3186 Processing sheet with id=AB3, first strand: chain 'B' and resid 3221 through 3225 removed outlier: 6.597A pdb=" N ILE B3211 " --> pdb=" O ILE B3224 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR B3202 " --> pdb=" O TYR B3459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 3235 through 3237 removed outlier: 6.728A pdb=" N ILE B3253 " --> pdb=" O ILE B3266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 3274 through 3280 removed outlier: 4.057A pdb=" N SER B3276 " --> pdb=" O LEU B3289 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B3296 " --> pdb=" O ILE B3309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 3325 through 3331 removed outlier: 4.805A pdb=" N GLY B3327 " --> pdb=" O ALA B3340 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B3348 " --> pdb=" O ILE B3361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 3371 through 3374 removed outlier: 4.290A pdb=" N ALA B3371 " --> pdb=" O ALA B3384 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B3391 " --> pdb=" O VAL B3404 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 3412 through 3418 removed outlier: 4.156A pdb=" N ALA B3414 " --> pdb=" O THR B3425 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B3432 " --> pdb=" O LEU B3446 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 3482 through 3484 Processing sheet with id=AC1, first strand: chain 'B' and resid 3499 through 3503 Processing sheet with id=AC2, first strand: chain 'B' and resid 3518 through 3520 Processing sheet with id=AC3, first strand: chain 'B' and resid 3560 through 3561 Processing sheet with id=AC4, first strand: chain 'B' and resid 3600 through 3602 Processing sheet with id=AC5, first strand: chain 'B' and resid 3641 through 3643 Processing sheet with id=AC6, first strand: chain 'B' and resid 3685 through 3687 Processing sheet with id=AC7, first strand: chain 'B' and resid 3726 through 3728 Processing sheet with id=AC8, first strand: chain 'B' and resid 3765 through 3767 Processing sheet with id=AC9, first strand: chain 'B' and resid 3804 through 3806 Processing sheet with id=AD1, first strand: chain 'B' and resid 3890 through 3892 199 hydrogen bonds defined for protein. 474 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: 4.12 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3149 1.33 - 1.46: 1797 1.46 - 1.58: 4716 1.58 - 1.70: 0 1.70 - 1.82: 148 Bond restraints: 9810 Sorted by residual: bond pdb=" N PHE B3838 " pdb=" CA PHE B3838 " ideal model delta sigma weight residual 1.455 1.486 -0.030 7.00e-03 2.04e+04 1.90e+01 bond pdb=" N ARG B3635 " pdb=" CA ARG B3635 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.34e-02 5.57e+03 8.14e+00 bond pdb=" N THR B3836 " pdb=" CA THR B3836 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.22e-02 6.72e+03 7.64e+00 bond pdb=" N ILE B3121 " pdb=" CA ILE B3121 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.52e+00 bond pdb=" CA SER B3359 " pdb=" CB SER B3359 " ideal model delta sigma weight residual 1.532 1.487 0.046 1.68e-02 3.54e+03 7.36e+00 ... (remaining 9805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 13037 2.85 - 5.71: 241 5.71 - 8.56: 5 8.56 - 11.41: 2 11.41 - 14.27: 1 Bond angle restraints: 13286 Sorted by residual: angle pdb=" C2 A2G B4703 " pdb=" C1 A2G B4703 " pdb=" O5 A2G B4703 " ideal model delta sigma weight residual 111.38 125.65 -14.27 3.00e+00 1.11e-01 2.26e+01 angle pdb=" CA THR B3356 " pdb=" C THR B3356 " pdb=" O THR B3356 " ideal model delta sigma weight residual 120.84 116.15 4.69 1.08e+00 8.57e-01 1.89e+01 angle pdb=" N ARG B3837 " pdb=" CA ARG B3837 " pdb=" C ARG B3837 " ideal model delta sigma weight residual 113.28 108.45 4.83 1.22e+00 6.72e-01 1.57e+01 angle pdb=" N CYS B3116 " pdb=" CA CYS B3116 " pdb=" C CYS B3116 " ideal model delta sigma weight residual 111.28 107.07 4.21 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N ASP B3118 " pdb=" CA ASP B3118 " pdb=" C ASP B3118 " ideal model delta sigma weight residual 111.71 107.31 4.40 1.15e+00 7.56e-01 1.46e+01 ... (remaining 13281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 5833 22.03 - 44.05: 506 44.05 - 66.07: 67 66.07 - 88.10: 57 88.10 - 110.12: 28 Dihedral angle restraints: 6491 sinusoidal: 3120 harmonic: 3371 Sorted by residual: dihedral pdb=" CB CYS B3741 " pdb=" SG CYS B3741 " pdb=" SG CYS B3756 " pdb=" CB CYS B3756 " ideal model delta sinusoidal sigma weight residual 93.00 158.14 -65.14 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS B3885 " pdb=" SG CYS B3885 " pdb=" SG CYS B3898 " pdb=" CB CYS B3898 " ideal model delta sinusoidal sigma weight residual 93.00 138.18 -45.18 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS B3514 " pdb=" SG CYS B3514 " pdb=" SG CYS B3527 " pdb=" CB CYS B3527 " ideal model delta sinusoidal sigma weight residual -86.00 -41.21 -44.79 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 6488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1165 0.063 - 0.126: 255 0.126 - 0.189: 20 0.189 - 0.252: 16 0.252 - 0.315: 3 Chirality restraints: 1459 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG A 2 " pdb=" O3 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.17e+01 chirality pdb=" C1 BMA D 3 " pdb=" O3 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.47e+01 ... (remaining 1456 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.254 2.00e-02 2.50e+03 2.12e-01 5.62e+02 pdb=" C7 NAG H 1 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.353 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.226 2.00e-02 2.50e+03 1.90e-01 4.50e+02 pdb=" C7 NAG F 1 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.317 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.211 2.00e-02 2.50e+03 1.77e-01 3.93e+02 pdb=" C7 NAG I 1 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.295 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.010 2.00e-02 2.50e+03 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 443 2.70 - 3.25: 10199 3.25 - 3.80: 15405 3.80 - 4.35: 20510 4.35 - 4.90: 32313 Nonbonded interactions: 78870 Sorted by model distance: nonbonded pdb=" OD1 ASN B3575 " pdb="CA CA B4718 " model vdw 2.150 2.510 nonbonded pdb=" OD2 ASP B3585 " pdb="CA CA B4718 " model vdw 2.167 2.510 nonbonded pdb=" OD2 ASP B3545 " pdb="CA CA B4717 " model vdw 2.169 2.510 nonbonded pdb=" OD2 ASP B3025 " pdb="CA CA B4710 " model vdw 2.169 2.510 nonbonded pdb=" OD1 ASP B3015 " pdb="CA CA B4710 " model vdw 2.187 2.510 ... (remaining 78865 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 'A' selection = chain 'D' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.170 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.120 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:3.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.450 9901 Z= 0.538 Angle : 0.896 14.266 13489 Z= 0.459 Chirality : 0.055 0.315 1459 Planarity : 0.012 0.212 1759 Dihedral : 19.136 110.123 4137 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.63 % Favored : 94.03 % Rotamer: Outliers : 1.73 % Allowed : 16.92 % Favored : 81.35 % 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: -0.39 (0.26), residues: 1155 helix: -1.20 (0.54), residues: 93 sheet: -0.82 (0.41), residues: 155 loop : 0.01 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B2925 HIS 0.005 0.001 HIS B3683 PHE 0.032 0.001 PHE B3891 TYR 0.020 0.002 TYR B3843 ARG 0.009 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00977 ( 9) link_NAG-ASN : angle 4.58071 ( 27) link_ALPHA1-6 : bond 0.00184 ( 3) link_ALPHA1-6 : angle 1.31264 ( 9) link_BETA1-4 : bond 0.00513 ( 12) link_BETA1-4 : angle 2.55494 ( 36) link_ALPHA1-3 : bond 0.00555 ( 3) link_ALPHA1-3 : angle 1.67916 ( 9) hydrogen bonds : bond 0.25017 ( 199) hydrogen bonds : angle 9.36168 ( 474) SS BOND : bond 0.00184 ( 58) SS BOND : angle 0.87308 ( 116) link_BETA1-3 : bond 0.00793 ( 2) link_BETA1-3 : angle 4.43381 ( 6) covalent geometry : bond 0.00505 ( 9810) covalent geometry : angle 0.85831 (13286) Misc. bond : bond 0.23141 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 17 residues processed: 75 average time/residue: 0.2453 time to fit residues: 26.1591 Evaluate side-chains 68 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain B residue 2884 PHE Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3064 ASP Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3589 VAL Chi-restraints excluded: chain B residue 3636 THR Chi-restraints excluded: chain B residue 3716 CYS Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3755 ASN Chi-restraints excluded: chain B residue 3762 SER Chi-restraints excluded: chain B residue 3870 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.0170 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN B2903 HIS B2924 ASN B2989 ASN ** B3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3378 ASN ** B3631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3811 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.135883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094831 restraints weight = 17683.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095465 restraints weight = 11335.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095814 restraints weight = 9043.352| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9901 Z= 0.123 Angle : 0.714 10.297 13489 Z= 0.340 Chirality : 0.049 0.327 1459 Planarity : 0.004 0.037 1759 Dihedral : 13.686 84.885 1963 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.17 % Allowed : 15.58 % Favored : 81.25 % 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: -0.36 (0.26), residues: 1155 helix: -1.19 (0.51), residues: 104 sheet: -0.74 (0.42), residues: 144 loop : 0.02 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B2925 HIS 0.003 0.001 HIS B3269 PHE 0.021 0.001 PHE B3891 TYR 0.010 0.001 TYR B3843 ARG 0.004 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00835 ( 9) link_NAG-ASN : angle 4.50830 ( 27) link_ALPHA1-6 : bond 0.00269 ( 3) link_ALPHA1-6 : angle 1.68988 ( 9) link_BETA1-4 : bond 0.00606 ( 12) link_BETA1-4 : angle 3.08115 ( 36) link_ALPHA1-3 : bond 0.01146 ( 3) link_ALPHA1-3 : angle 2.09911 ( 9) hydrogen bonds : bond 0.04473 ( 199) hydrogen bonds : angle 6.52632 ( 474) SS BOND : bond 0.00201 ( 58) SS BOND : angle 0.75150 ( 116) link_BETA1-3 : bond 0.01377 ( 2) link_BETA1-3 : angle 3.97738 ( 6) covalent geometry : bond 0.00258 ( 9810) covalent geometry : angle 0.65861 (13286) Misc. bond : bond 0.00038 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2921 ILE cc_start: -0.0757 (OUTLIER) cc_final: -0.1184 (pp) REVERT: B 2993 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.5674 (ptm160) REVERT: B 3167 GLN cc_start: 0.8657 (mt0) cc_final: 0.8420 (mt0) REVERT: B 3223 LEU cc_start: 0.8305 (tt) cc_final: 0.7971 (tp) REVERT: B 3433 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: B 3513 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6900 (tpt) outliers start: 33 outliers final: 17 residues processed: 94 average time/residue: 0.2290 time to fit residues: 30.8555 Evaluate side-chains 74 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3362 ILE Chi-restraints excluded: chain B residue 3377 THR Chi-restraints excluded: chain B residue 3378 ASN Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3433 GLU Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3682 ASN Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3842 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2959 ASN B3336 HIS ** B3631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093715 restraints weight = 17961.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094347 restraints weight = 12204.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094556 restraints weight = 9395.160| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9901 Z= 0.148 Angle : 0.693 10.742 13489 Z= 0.331 Chirality : 0.048 0.281 1459 Planarity : 0.004 0.040 1759 Dihedral : 11.672 78.533 1947 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.08 % Allowed : 16.35 % Favored : 80.58 % 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: -0.42 (0.26), residues: 1155 helix: -1.10 (0.51), residues: 104 sheet: -0.86 (0.41), residues: 149 loop : -0.01 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B2925 HIS 0.004 0.001 HIS B3269 PHE 0.014 0.001 PHE B3891 TYR 0.010 0.001 TYR B3338 ARG 0.005 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 9) link_NAG-ASN : angle 4.55633 ( 27) link_ALPHA1-6 : bond 0.00271 ( 3) link_ALPHA1-6 : angle 1.85673 ( 9) link_BETA1-4 : bond 0.00577 ( 12) link_BETA1-4 : angle 2.87661 ( 36) link_ALPHA1-3 : bond 0.01112 ( 3) link_ALPHA1-3 : angle 1.80296 ( 9) hydrogen bonds : bond 0.04127 ( 199) hydrogen bonds : angle 6.09018 ( 474) SS BOND : bond 0.00301 ( 58) SS BOND : angle 0.86475 ( 116) link_BETA1-3 : bond 0.01271 ( 2) link_BETA1-3 : angle 3.75766 ( 6) covalent geometry : bond 0.00334 ( 9810) covalent geometry : angle 0.63669 (13286) Misc. bond : bond 0.00086 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2921 ILE cc_start: -0.0783 (OUTLIER) cc_final: -0.1185 (pp) REVERT: B 3047 ILE cc_start: 0.6184 (OUTLIER) cc_final: 0.5912 (tt) REVERT: B 3223 LEU cc_start: 0.8371 (tt) cc_final: 0.8054 (tp) REVERT: B 3513 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6944 (tpt) outliers start: 32 outliers final: 22 residues processed: 80 average time/residue: 0.2521 time to fit residues: 28.4096 Evaluate side-chains 76 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2992 MET Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3047 ILE Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3177 ILE Chi-restraints excluded: chain B residue 3348 ILE Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3556 ARG Chi-restraints excluded: chain B residue 3557 LEU Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3755 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 49 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 114 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3207 ASN B3631 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.136428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094876 restraints weight = 17731.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095221 restraints weight = 12411.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096156 restraints weight = 8723.450| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9901 Z= 0.112 Angle : 0.646 11.122 13489 Z= 0.307 Chirality : 0.047 0.292 1459 Planarity : 0.004 0.040 1759 Dihedral : 9.131 65.215 1947 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.37 % Allowed : 16.35 % Favored : 80.29 % 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: -0.35 (0.26), residues: 1155 helix: -1.00 (0.50), residues: 104 sheet: -0.96 (0.38), residues: 171 loop : 0.09 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B2925 HIS 0.008 0.001 HIS B3552 PHE 0.012 0.001 PHE B3891 TYR 0.008 0.001 TYR B3382 ARG 0.004 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 9) link_NAG-ASN : angle 4.41561 ( 27) link_ALPHA1-6 : bond 0.00580 ( 3) link_ALPHA1-6 : angle 2.14159 ( 9) link_BETA1-4 : bond 0.00561 ( 12) link_BETA1-4 : angle 2.77988 ( 36) link_ALPHA1-3 : bond 0.01146 ( 3) link_ALPHA1-3 : angle 1.85476 ( 9) hydrogen bonds : bond 0.03447 ( 199) hydrogen bonds : angle 5.61098 ( 474) SS BOND : bond 0.00176 ( 58) SS BOND : angle 0.76450 ( 116) link_BETA1-3 : bond 0.01045 ( 2) link_BETA1-3 : angle 3.10812 ( 6) covalent geometry : bond 0.00243 ( 9810) covalent geometry : angle 0.59009 (13286) Misc. bond : bond 0.00084 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2921 ILE cc_start: -0.0546 (OUTLIER) cc_final: -0.0968 (pp) REVERT: B 3223 LEU cc_start: 0.8338 (tt) cc_final: 0.8034 (tp) REVERT: B 3509 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8302 (tm) REVERT: B 3513 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6909 (tpt) REVERT: B 3672 GLU cc_start: 0.8393 (tt0) cc_final: 0.8181 (tt0) REVERT: B 3689 LYS cc_start: 0.7730 (mttp) cc_final: 0.7467 (mttp) REVERT: B 3745 ASP cc_start: 0.7936 (t0) cc_final: 0.7651 (t0) outliers start: 35 outliers final: 22 residues processed: 93 average time/residue: 0.2407 time to fit residues: 31.8034 Evaluate side-chains 79 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2884 PHE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2992 MET Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3000 PHE Chi-restraints excluded: chain B residue 3041 CYS Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3334 ARG Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3377 THR Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3509 LEU Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3749 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 108 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3552 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.136389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094803 restraints weight = 17852.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095111 restraints weight = 13012.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096499 restraints weight = 8669.631| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9901 Z= 0.113 Angle : 0.638 11.229 13489 Z= 0.305 Chirality : 0.046 0.289 1459 Planarity : 0.004 0.042 1759 Dihedral : 8.705 59.619 1947 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.56 % Allowed : 16.63 % Favored : 79.81 % 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: -0.33 (0.26), residues: 1155 helix: -1.02 (0.50), residues: 104 sheet: -0.98 (0.38), residues: 173 loop : 0.13 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2925 HIS 0.007 0.001 HIS B3552 PHE 0.010 0.001 PHE B3205 TYR 0.008 0.001 TYR B3382 ARG 0.006 0.000 ARG C 58 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 9) link_NAG-ASN : angle 4.17225 ( 27) link_ALPHA1-6 : bond 0.00487 ( 3) link_ALPHA1-6 : angle 1.68383 ( 9) link_BETA1-4 : bond 0.00474 ( 12) link_BETA1-4 : angle 2.67862 ( 36) link_ALPHA1-3 : bond 0.01191 ( 3) link_ALPHA1-3 : angle 1.89085 ( 9) hydrogen bonds : bond 0.03297 ( 199) hydrogen bonds : angle 5.56279 ( 474) SS BOND : bond 0.00167 ( 58) SS BOND : angle 0.69652 ( 116) link_BETA1-3 : bond 0.00926 ( 2) link_BETA1-3 : angle 3.07141 ( 6) covalent geometry : bond 0.00246 ( 9810) covalent geometry : angle 0.58739 (13286) Misc. bond : bond 0.00085 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 97 LYS cc_start: 0.3801 (OUTLIER) cc_final: 0.3503 (pttm) REVERT: B 2921 ILE cc_start: -0.0404 (OUTLIER) cc_final: -0.0845 (pp) REVERT: B 3050 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: B 3223 LEU cc_start: 0.8321 (tt) cc_final: 0.8017 (tp) REVERT: B 3509 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8370 (tm) REVERT: B 3513 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6969 (tpt) REVERT: B 3556 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6765 (mmt-90) REVERT: B 3573 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8297 (mm) REVERT: B 3592 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6909 (tm-30) REVERT: B 3745 ASP cc_start: 0.7916 (t0) cc_final: 0.7591 (t0) REVERT: B 3827 ASP cc_start: 0.7967 (t0) cc_final: 0.7735 (t0) outliers start: 37 outliers final: 26 residues processed: 90 average time/residue: 0.2477 time to fit residues: 31.1506 Evaluate side-chains 87 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2884 PHE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2992 MET Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3000 PHE Chi-restraints excluded: chain B residue 3041 CYS Chi-restraints excluded: chain B residue 3050 PHE Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3334 ARG Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3377 THR Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3509 LEU Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3556 ARG Chi-restraints excluded: chain B residue 3573 LEU Chi-restraints excluded: chain B residue 3682 ASN Chi-restraints excluded: chain B residue 3719 VAL Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3755 ASN Chi-restraints excluded: chain B residue 3870 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3552 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096250 restraints weight = 17760.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095549 restraints weight = 10579.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095242 restraints weight = 8887.308| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9901 Z= 0.176 Angle : 0.683 11.232 13489 Z= 0.329 Chirality : 0.048 0.289 1459 Planarity : 0.004 0.046 1759 Dihedral : 8.610 58.030 1947 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.71 % Allowed : 16.25 % Favored : 79.04 % 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: -0.45 (0.26), residues: 1155 helix: -1.08 (0.48), residues: 104 sheet: -1.10 (0.38), residues: 171 loop : 0.05 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B2925 HIS 0.007 0.001 HIS B3552 PHE 0.014 0.001 PHE B3393 TYR 0.010 0.002 TYR B2882 ARG 0.005 0.001 ARG B3009 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 9) link_NAG-ASN : angle 4.29333 ( 27) link_ALPHA1-6 : bond 0.00287 ( 3) link_ALPHA1-6 : angle 1.94943 ( 9) link_BETA1-4 : bond 0.00477 ( 12) link_BETA1-4 : angle 2.63972 ( 36) link_ALPHA1-3 : bond 0.01041 ( 3) link_ALPHA1-3 : angle 1.96830 ( 9) hydrogen bonds : bond 0.03427 ( 199) hydrogen bonds : angle 5.77243 ( 474) SS BOND : bond 0.00225 ( 58) SS BOND : angle 0.76104 ( 116) link_BETA1-3 : bond 0.01114 ( 2) link_BETA1-3 : angle 3.13203 ( 6) covalent geometry : bond 0.00401 ( 9810) covalent geometry : angle 0.63468 (13286) Misc. bond : bond 0.00089 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 53 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 97 LYS cc_start: 0.4326 (OUTLIER) cc_final: 0.4001 (pttm) REVERT: B 2921 ILE cc_start: -0.0373 (OUTLIER) cc_final: -0.0858 (pp) REVERT: B 3223 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8054 (tp) REVERT: B 3509 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8383 (tm) REVERT: B 3513 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6889 (tpt) REVERT: B 3573 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8426 (mm) REVERT: B 3592 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6915 (tm-30) REVERT: B 3689 LYS cc_start: 0.7729 (mttp) cc_final: 0.7448 (mttp) outliers start: 49 outliers final: 33 residues processed: 89 average time/residue: 0.2476 time to fit residues: 31.3386 Evaluate side-chains 89 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 50 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2884 PHE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2992 MET Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3041 CYS Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3077 CYS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3177 ILE Chi-restraints excluded: chain B residue 3178 CYS Chi-restraints excluded: chain B residue 3223 LEU Chi-restraints excluded: chain B residue 3334 ARG Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3377 THR Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3444 VAL Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3508 THR Chi-restraints excluded: chain B residue 3509 LEU Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3556 ARG Chi-restraints excluded: chain B residue 3573 LEU Chi-restraints excluded: chain B residue 3682 ASN Chi-restraints excluded: chain B residue 3719 VAL Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3749 ASP Chi-restraints excluded: chain B residue 3755 ASN Chi-restraints excluded: chain B residue 3870 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 chunk 109 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095233 restraints weight = 17931.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095326 restraints weight = 11857.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095650 restraints weight = 9065.207| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9901 Z= 0.110 Angle : 0.636 11.494 13489 Z= 0.304 Chirality : 0.046 0.291 1459 Planarity : 0.004 0.046 1759 Dihedral : 8.134 59.983 1947 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.37 % Allowed : 17.21 % Favored : 79.42 % 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: -0.32 (0.26), residues: 1155 helix: -0.98 (0.48), residues: 105 sheet: -1.04 (0.38), residues: 173 loop : 0.15 (0.23), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2925 HIS 0.002 0.001 HIS B3269 PHE 0.011 0.001 PHE B3205 TYR 0.009 0.001 TYR B3221 ARG 0.004 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 9) link_NAG-ASN : angle 4.17375 ( 27) link_ALPHA1-6 : bond 0.00495 ( 3) link_ALPHA1-6 : angle 1.81772 ( 9) link_BETA1-4 : bond 0.00493 ( 12) link_BETA1-4 : angle 2.50756 ( 36) link_ALPHA1-3 : bond 0.01230 ( 3) link_ALPHA1-3 : angle 1.75880 ( 9) hydrogen bonds : bond 0.03177 ( 199) hydrogen bonds : angle 5.61581 ( 474) SS BOND : bond 0.00165 ( 58) SS BOND : angle 0.69904 ( 116) link_BETA1-3 : bond 0.00998 ( 2) link_BETA1-3 : angle 2.88836 ( 6) covalent geometry : bond 0.00241 ( 9810) covalent geometry : angle 0.58828 (13286) Misc. bond : bond 0.00090 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ARG cc_start: 0.4835 (mtp85) cc_final: 0.3623 (mmp80) REVERT: C 97 LYS cc_start: 0.4236 (OUTLIER) cc_final: 0.3905 (pttm) REVERT: B 2921 ILE cc_start: -0.0364 (OUTLIER) cc_final: -0.0795 (pp) REVERT: B 3050 PHE cc_start: 0.7383 (m-80) cc_final: 0.7078 (m-10) REVERT: B 3223 LEU cc_start: 0.8279 (tt) cc_final: 0.8004 (tp) REVERT: B 3509 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8364 (tm) REVERT: B 3513 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6862 (tpt) REVERT: B 3573 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8301 (mm) REVERT: B 3592 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6919 (tm-30) REVERT: B 3689 LYS cc_start: 0.7813 (mttp) cc_final: 0.7494 (mttp) REVERT: B 3745 ASP cc_start: 0.7948 (t0) cc_final: 0.7547 (t0) outliers start: 35 outliers final: 25 residues processed: 85 average time/residue: 0.2802 time to fit residues: 33.4291 Evaluate side-chains 83 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2884 PHE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2984 LEU Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3000 PHE Chi-restraints excluded: chain B residue 3041 CYS Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3077 CYS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3377 THR Chi-restraints excluded: chain B residue 3378 ASN Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3509 LEU Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3556 ARG Chi-restraints excluded: chain B residue 3573 LEU Chi-restraints excluded: chain B residue 3719 VAL Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3755 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 0.0000 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 70 optimal weight: 0.0040 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3552 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096948 restraints weight = 18114.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096919 restraints weight = 10006.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096174 restraints weight = 8785.144| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9901 Z= 0.117 Angle : 0.636 11.509 13489 Z= 0.304 Chirality : 0.046 0.290 1459 Planarity : 0.004 0.046 1759 Dihedral : 7.862 58.510 1947 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.46 % Allowed : 17.31 % Favored : 79.23 % 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: -0.29 (0.26), residues: 1155 helix: -0.95 (0.49), residues: 105 sheet: -1.06 (0.38), residues: 173 loop : 0.18 (0.23), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2925 HIS 0.008 0.001 HIS B3552 PHE 0.010 0.001 PHE B3393 TYR 0.009 0.001 TYR B3338 ARG 0.004 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 9) link_NAG-ASN : angle 4.15612 ( 27) link_ALPHA1-6 : bond 0.00471 ( 3) link_ALPHA1-6 : angle 1.87949 ( 9) link_BETA1-4 : bond 0.00493 ( 12) link_BETA1-4 : angle 2.47743 ( 36) link_ALPHA1-3 : bond 0.01166 ( 3) link_ALPHA1-3 : angle 1.76617 ( 9) hydrogen bonds : bond 0.03097 ( 199) hydrogen bonds : angle 5.56200 ( 474) SS BOND : bond 0.00166 ( 58) SS BOND : angle 0.69367 ( 116) link_BETA1-3 : bond 0.01009 ( 2) link_BETA1-3 : angle 2.93195 ( 6) covalent geometry : bond 0.00260 ( 9810) covalent geometry : angle 0.58840 (13286) Misc. bond : bond 0.00089 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ARG cc_start: 0.4992 (mtp85) cc_final: 0.3881 (mmp80) REVERT: C 97 LYS cc_start: 0.4220 (OUTLIER) cc_final: 0.3918 (pttm) REVERT: B 2921 ILE cc_start: -0.0335 (OUTLIER) cc_final: -0.0793 (pp) REVERT: B 3050 PHE cc_start: 0.7287 (m-80) cc_final: 0.6977 (m-10) REVERT: B 3077 CYS cc_start: 0.4101 (OUTLIER) cc_final: 0.1795 (p) REVERT: B 3223 LEU cc_start: 0.8233 (tt) cc_final: 0.7978 (tp) REVERT: B 3509 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8374 (tm) REVERT: B 3513 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6838 (tpt) REVERT: B 3573 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8331 (mm) REVERT: B 3592 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6904 (tm-30) REVERT: B 3689 LYS cc_start: 0.7906 (mttp) cc_final: 0.7638 (mttp) REVERT: B 3745 ASP cc_start: 0.7964 (t0) cc_final: 0.7548 (t0) REVERT: B 3827 ASP cc_start: 0.7943 (t0) cc_final: 0.7740 (t0) outliers start: 36 outliers final: 26 residues processed: 86 average time/residue: 0.2390 time to fit residues: 28.7491 Evaluate side-chains 87 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2884 PHE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2984 LEU Chi-restraints excluded: chain B residue 2992 MET Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3041 CYS Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3077 CYS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3177 ILE Chi-restraints excluded: chain B residue 3178 CYS Chi-restraints excluded: chain B residue 3334 ARG Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3509 LEU Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3556 ARG Chi-restraints excluded: chain B residue 3573 LEU Chi-restraints excluded: chain B residue 3719 VAL Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3755 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 83 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3552 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.135972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094648 restraints weight = 17813.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095173 restraints weight = 11608.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095679 restraints weight = 8019.120| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9901 Z= 0.112 Angle : 0.630 11.523 13489 Z= 0.301 Chirality : 0.046 0.292 1459 Planarity : 0.004 0.046 1759 Dihedral : 7.475 58.603 1947 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.37 % Allowed : 17.60 % Favored : 79.04 % 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: -0.23 (0.26), residues: 1155 helix: -0.84 (0.49), residues: 105 sheet: -1.03 (0.38), residues: 173 loop : 0.21 (0.23), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B3424 HIS 0.007 0.001 HIS B3552 PHE 0.036 0.001 PHE B3082 TYR 0.009 0.001 TYR B3382 ARG 0.004 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 9) link_NAG-ASN : angle 4.11620 ( 27) link_ALPHA1-6 : bond 0.00517 ( 3) link_ALPHA1-6 : angle 1.78581 ( 9) link_BETA1-4 : bond 0.00493 ( 12) link_BETA1-4 : angle 2.43517 ( 36) link_ALPHA1-3 : bond 0.01126 ( 3) link_ALPHA1-3 : angle 1.67360 ( 9) hydrogen bonds : bond 0.03027 ( 199) hydrogen bonds : angle 5.53008 ( 474) SS BOND : bond 0.00160 ( 58) SS BOND : angle 0.67577 ( 116) link_BETA1-3 : bond 0.00980 ( 2) link_BETA1-3 : angle 2.87915 ( 6) covalent geometry : bond 0.00248 ( 9810) covalent geometry : angle 0.58412 (13286) Misc. bond : bond 0.00089 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ARG cc_start: 0.4791 (mtp85) cc_final: 0.3937 (mmp80) REVERT: C 97 LYS cc_start: 0.4204 (OUTLIER) cc_final: 0.3897 (pttm) REVERT: B 2921 ILE cc_start: -0.0367 (OUTLIER) cc_final: -0.0798 (pp) REVERT: B 3050 PHE cc_start: 0.7364 (m-80) cc_final: 0.7063 (m-10) REVERT: B 3077 CYS cc_start: 0.4207 (OUTLIER) cc_final: 0.1850 (p) REVERT: B 3223 LEU cc_start: 0.8244 (tt) cc_final: 0.7980 (tp) REVERT: B 3509 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8376 (tm) REVERT: B 3513 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6829 (tpt) REVERT: B 3573 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8299 (mm) REVERT: B 3592 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6911 (tm-30) REVERT: B 3689 LYS cc_start: 0.7931 (mttp) cc_final: 0.7704 (mttp) REVERT: B 3827 ASP cc_start: 0.7957 (t0) cc_final: 0.7627 (t0) REVERT: B 3919 GLU cc_start: 0.5658 (OUTLIER) cc_final: 0.4999 (mp0) outliers start: 35 outliers final: 25 residues processed: 85 average time/residue: 0.2517 time to fit residues: 29.5160 Evaluate side-chains 90 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2884 PHE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2992 MET Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3041 CYS Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3077 CYS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3177 ILE Chi-restraints excluded: chain B residue 3178 CYS Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3509 LEU Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3556 ARG Chi-restraints excluded: chain B residue 3573 LEU Chi-restraints excluded: chain B residue 3589 VAL Chi-restraints excluded: chain B residue 3719 VAL Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3755 ASN Chi-restraints excluded: chain B residue 3919 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 0.0470 chunk 100 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 0.0970 chunk 22 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3552 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.136293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095562 restraints weight = 17863.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096081 restraints weight = 10340.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096786 restraints weight = 7839.480| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9901 Z= 0.106 Angle : 0.626 11.643 13489 Z= 0.299 Chirality : 0.046 0.296 1459 Planarity : 0.004 0.046 1759 Dihedral : 7.246 58.445 1947 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.46 % Allowed : 17.40 % Favored : 79.13 % 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: -0.15 (0.26), residues: 1155 helix: -0.73 (0.50), residues: 105 sheet: -0.95 (0.39), residues: 173 loop : 0.26 (0.23), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 66 HIS 0.007 0.001 HIS B3552 PHE 0.026 0.001 PHE B3082 TYR 0.008 0.001 TYR B3382 ARG 0.004 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 9) link_NAG-ASN : angle 4.05408 ( 27) link_ALPHA1-6 : bond 0.00410 ( 3) link_ALPHA1-6 : angle 1.63040 ( 9) link_BETA1-4 : bond 0.00497 ( 12) link_BETA1-4 : angle 2.39292 ( 36) link_ALPHA1-3 : bond 0.01061 ( 3) link_ALPHA1-3 : angle 1.58916 ( 9) hydrogen bonds : bond 0.03005 ( 199) hydrogen bonds : angle 5.44452 ( 474) SS BOND : bond 0.00150 ( 58) SS BOND : angle 0.64315 ( 116) link_BETA1-3 : bond 0.00963 ( 2) link_BETA1-3 : angle 2.81646 ( 6) covalent geometry : bond 0.00233 ( 9810) covalent geometry : angle 0.58116 (13286) Misc. bond : bond 0.00089 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ARG cc_start: 0.4776 (mtp85) cc_final: 0.3887 (mmp80) REVERT: C 97 LYS cc_start: 0.4207 (OUTLIER) cc_final: 0.3882 (pttm) REVERT: B 2921 ILE cc_start: -0.0720 (OUTLIER) cc_final: -0.1131 (pp) REVERT: B 3050 PHE cc_start: 0.7384 (m-80) cc_final: 0.7034 (m-10) REVERT: B 3077 CYS cc_start: 0.4316 (OUTLIER) cc_final: 0.1979 (p) REVERT: B 3223 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7981 (tp) REVERT: B 3509 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8361 (tm) REVERT: B 3513 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6843 (tpt) REVERT: B 3556 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6763 (mmt-90) REVERT: B 3573 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 3592 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6922 (tm-30) REVERT: B 3689 LYS cc_start: 0.7961 (mttp) cc_final: 0.7669 (mttp) REVERT: B 3827 ASP cc_start: 0.7966 (t0) cc_final: 0.7606 (t0) REVERT: B 3919 GLU cc_start: 0.5626 (OUTLIER) cc_final: 0.4985 (mp0) outliers start: 36 outliers final: 26 residues processed: 87 average time/residue: 0.2975 time to fit residues: 36.1662 Evaluate side-chains 91 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 2879 ILE Chi-restraints excluded: chain B residue 2884 PHE Chi-restraints excluded: chain B residue 2921 ILE Chi-restraints excluded: chain B residue 2992 MET Chi-restraints excluded: chain B residue 2993 ARG Chi-restraints excluded: chain B residue 3041 CYS Chi-restraints excluded: chain B residue 3063 SER Chi-restraints excluded: chain B residue 3077 CYS Chi-restraints excluded: chain B residue 3118 ASP Chi-restraints excluded: chain B residue 3145 LEU Chi-restraints excluded: chain B residue 3150 ARG Chi-restraints excluded: chain B residue 3173 VAL Chi-restraints excluded: chain B residue 3177 ILE Chi-restraints excluded: chain B residue 3178 CYS Chi-restraints excluded: chain B residue 3223 LEU Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3426 ASP Chi-restraints excluded: chain B residue 3449 THR Chi-restraints excluded: chain B residue 3505 ARG Chi-restraints excluded: chain B residue 3509 LEU Chi-restraints excluded: chain B residue 3513 MET Chi-restraints excluded: chain B residue 3556 ARG Chi-restraints excluded: chain B residue 3573 LEU Chi-restraints excluded: chain B residue 3589 VAL Chi-restraints excluded: chain B residue 3719 VAL Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3737 LEU Chi-restraints excluded: chain B residue 3755 ASN Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3919 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B3552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.135644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093802 restraints weight = 17785.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094208 restraints weight = 13825.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095576 restraints weight = 8853.199| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9901 Z= 0.122 Angle : 0.633 11.386 13489 Z= 0.303 Chirality : 0.046 0.294 1459 Planarity : 0.004 0.047 1759 Dihedral : 7.296 57.841 1947 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.46 % Allowed : 17.50 % Favored : 79.04 % 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: -0.16 (0.26), residues: 1155 helix: -0.61 (0.50), residues: 105 sheet: -1.03 (0.39), residues: 171 loop : 0.25 (0.23), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 66 HIS 0.006 0.001 HIS B3552 PHE 0.026 0.001 PHE B3082 TYR 0.008 0.001 TYR B3338 ARG 0.004 0.000 ARG B3016 Details of bonding type rmsd link_NAG-ASN : bond 0.00693 ( 9) link_NAG-ASN : angle 4.04011 ( 27) link_ALPHA1-6 : bond 0.00254 ( 3) link_ALPHA1-6 : angle 1.75707 ( 9) link_BETA1-4 : bond 0.00478 ( 12) link_BETA1-4 : angle 2.39901 ( 36) link_ALPHA1-3 : bond 0.00944 ( 3) link_ALPHA1-3 : angle 1.62869 ( 9) hydrogen bonds : bond 0.02967 ( 199) hydrogen bonds : angle 5.49010 ( 474) SS BOND : bond 0.00167 ( 58) SS BOND : angle 0.66187 ( 116) link_BETA1-3 : bond 0.00974 ( 2) link_BETA1-3 : angle 2.81460 ( 6) covalent geometry : bond 0.00274 ( 9810) covalent geometry : angle 0.58903 (13286) Misc. bond : bond 0.00089 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3470.22 seconds wall clock time: 62 minutes 15.29 seconds (3735.29 seconds total)