Starting phenix.real_space_refine on Fri Jul 3 04:24:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx9_36693/07_2026/8jx9_36693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx9_36693/07_2026/8jx9_36693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jx9_36693/07_2026/8jx9_36693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx9_36693/07_2026/8jx9_36693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jx9_36693/07_2026/8jx9_36693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx9_36693/07_2026/8jx9_36693.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 20 9.91 5 S 149 5.16 5 C 7194 2.51 5 N 2057 2.21 5 O 2402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11822 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2904 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 20, 'TRANS': 340} Chain: "B" Number of atoms: 8455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8455 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 53, 'TRANS': 1023} Chain breaks: 1 Chain: "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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 98 Ad-hoc single atom residues: {' CA': 20} Unusual residues: {'A2G': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 20 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.59, per 1000 atoms: 0.30 Number of scatterers: 11822 At special positions: 0 Unit cell: (117.113, 119.935, 162.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 20 19.99 S 149 16.00 O 2402 8.00 N 2057 7.00 C 7194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=64, symmetry=0 Simple disulfide: pdb=" SG CYS A4336 " - pdb=" SG CYS A4344 " distance=2.03 Simple disulfide: pdb=" SG CYS A4340 " - pdb=" SG CYS A4353 " distance=2.03 Simple disulfide: pdb=" SG CYS A4355 " - pdb=" SG CYS A4369 " distance=2.03 Simple disulfide: pdb=" SG CYS A4383 " - pdb=" SG CYS A4391 " distance=2.03 Simple disulfide: pdb=" SG CYS A4385 " - pdb=" SG CYS A4401 " distance=2.03 Simple disulfide: pdb=" SG CYS A4403 " - pdb=" SG CYS A4412 " distance=2.03 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1244 " distance=2.03 Simple disulfide: pdb=" SG CYS B1238 " - pdb=" SG CYS B1257 " distance=2.03 Simple disulfide: pdb=" SG CYS B1251 " - pdb=" SG CYS B1267 " 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B3116 " - pdb=" SG CYS B3128 " distance=2.03 Simple disulfide: pdb=" SG CYS B3124 " - pdb=" SG CYS B3137 " distance=2.02 Simple disulfide: pdb=" SG CYS B3139 " - pdb=" SG CYS B3152 " distance=2.04 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=2.04 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 B3637 " - pdb=" SG CYS B3649 " 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=2.04 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=5, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG B4701 " - " ASN B3448 " " NAG B4702 " - " ASN B3682 " " NAG C 1 " - " ASN B3127 " " 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=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 542.6 milliseconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 35 sheets defined 11.6% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 4324 through 4328 Processing helix chain 'B' and resid 1248 through 1250 No H-bonds generated for 'chain 'B' and resid 1248 through 1250' Processing helix chain 'B' and resid 1260 through 1264 removed outlier: 3.838A pdb=" N HIS B1264 " --> pdb=" O SER B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2924 through 2926 No H-bonds generated for 'chain 'B' and resid 2924 through 2926' Processing helix chain 'B' and resid 2983 through 2987 Processing helix chain 'B' and resid 3009 through 3013 removed outlier: 3.503A pdb=" N ARG B3013 " --> pdb=" O GLN B3010 " (cutoff:3.500A) Processing helix chain 'B' and resid 3048 through 3052 Processing helix chain 'B' and resid 3062 through 3065 Processing helix chain 'B' and resid 3066 through 3071 Processing helix chain 'B' and resid 3091 through 3095 removed outlier: 3.651A pdb=" N VAL B3095 " --> pdb=" O MET B3092 " (cutoff:3.500A) Processing helix chain 'B' and resid 3105 through 3109 Processing helix chain 'B' and resid 3156 through 3161 Processing helix chain 'B' and resid 3162 through 3165 Processing helix chain 'B' and resid 3460 through 3464 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 3664 through 3668 removed outlier: 4.283A pdb=" N ASP B3667 " --> pdb=" O ASP B3664 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3674 Processing helix chain 'B' and resid 3675 through 3679 removed outlier: 3.581A pdb=" N ASN B3679 " --> pdb=" O ALA B3676 " (cutoff:3.500A) 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 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 3750 through 3754 removed outlier: 3.510A pdb=" N GLU B3754 " --> pdb=" O SER B3751 " (cutoff:3.500A) 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 3789 through 3793 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 3828 through 3833 removed outlier: 4.225A pdb=" N ALA B3833 " --> pdb=" O SER B3829 " (cutoff:3.500A) Processing helix chain 'B' and resid 3858 through 3862 removed outlier: 3.538A pdb=" N TRP B3861 " --> pdb=" O GLN B3858 " (cutoff:3.500A) Processing helix chain 'B' and resid 3876 through 3881 Processing helix chain 'B' and resid 3902 through 3904 No H-bonds generated for 'chain 'B' and resid 3902 through 3904' Processing sheet with id=AA1, first strand: chain 'A' and resid 4076 through 4077 removed outlier: 4.408A pdb=" N LYS A4068 " --> pdb=" O SER A4077 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4086 through 4092 removed outlier: 4.830A pdb=" N THR A4088 " --> pdb=" O THR A4106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4148 through 4152 removed outlier: 4.045A pdb=" N GLY A4148 " --> pdb=" O SER A4161 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A4171 " --> pdb=" O ILE A4158 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP A4160 " --> pdb=" O GLU A4169 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A4168 " --> pdb=" O LEU A4181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 4189 through 4195 removed outlier: 5.432A pdb=" N ALA A4191 " --> pdb=" O THR A4204 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A4204 " --> pdb=" O ALA A4191 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE A4212 " --> pdb=" O LEU A4225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 4236 through 4239 removed outlier: 6.971A pdb=" N ILE A4256 " --> pdb=" O ILE A4269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 4276 through 4282 removed outlier: 4.871A pdb=" N SER A4278 " --> pdb=" O VAL A4289 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A4289 " --> pdb=" O SER A4278 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A4288 " --> pdb=" O TRP A4297 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A4295 " --> pdb=" O ALA A4290 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A4296 " --> pdb=" O VAL A4310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4343 through 4347 Processing sheet with id=AA8, first strand: chain 'A' and resid 4390 through 4393 Processing sheet with id=AA9, first strand: chain 'B' and resid 1235 through 1237 Processing sheet with id=AB1, first strand: chain 'B' and resid 2912 through 2914 Processing sheet with id=AB2, first strand: chain 'B' and resid 2955 through 2956 Processing sheet with id=AB3, first strand: chain 'B' and resid 3000 through 3001 Processing sheet with id=AB4, first strand: chain 'B' and resid 3039 through 3040 Processing sheet with id=AB5, first strand: chain 'B' and resid 3127 through 3130 Processing sheet with id=AB6, first strand: chain 'B' and resid 3143 through 3145 Processing sheet with id=AB7, first strand: chain 'B' and resid 3169 through 3172 Processing sheet with id=AB8, first strand: chain 'B' and resid 3184 through 3186 Processing sheet with id=AB9, first strand: chain 'B' and resid 3221 through 3226 removed outlier: 6.719A pdb=" N ILE B3211 " --> pdb=" O ILE B3224 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B3202 " --> pdb=" O TYR B3459 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP B3455 " --> pdb=" O SER B3206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 3235 through 3237 removed outlier: 3.587A pdb=" N TRP B3245 " --> pdb=" O GLU B3254 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B3253 " --> pdb=" O ILE B3266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 3274 through 3280 removed outlier: 4.398A pdb=" N SER B3276 " --> pdb=" O LEU B3289 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B3296 " --> pdb=" O ILE B3309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 3325 through 3331 removed outlier: 4.645A pdb=" N GLY B3327 " --> pdb=" O ALA B3340 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B3348 " --> pdb=" O ILE B3361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 3371 through 3375 removed outlier: 3.839A pdb=" N ALA B3371 " --> pdb=" O ALA B3384 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B3384 " --> pdb=" O ALA B3371 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE B3391 " --> pdb=" O VAL B3404 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 3412 through 3418 removed outlier: 4.135A pdb=" N ALA B3414 " --> pdb=" O THR B3425 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B3432 " --> pdb=" O LEU B3446 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 3482 through 3484 Processing sheet with id=AC7, first strand: chain 'B' and resid 3499 through 3503 Processing sheet with id=AC8, first strand: chain 'B' and resid 3518 through 3520 Processing sheet with id=AC9, first strand: chain 'B' and resid 3560 through 3561 Processing sheet with id=AD1, first strand: chain 'B' and resid 3600 through 3602 Processing sheet with id=AD2, first strand: chain 'B' and resid 3641 through 3643 Processing sheet with id=AD3, first strand: chain 'B' and resid 3685 through 3687 Processing sheet with id=AD4, first strand: chain 'B' and resid 3726 through 3728 Processing sheet with id=AD5, first strand: chain 'B' and resid 3765 through 3767 Processing sheet with id=AD6, first strand: chain 'B' and resid 3804 through 3806 Processing sheet with id=AD7, first strand: chain 'B' and resid 3849 through 3850 Processing sheet with id=AD8, first strand: chain 'B' and resid 3890 through 3892 251 hydrogen bonds defined for protein. 546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4001 1.34 - 1.46: 2716 1.46 - 1.58: 5197 1.58 - 1.70: 0 1.70 - 1.83: 168 Bond restraints: 12082 Sorted by residual: bond pdb=" N THR B3636 " pdb=" CA THR B3636 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.63e+00 bond pdb=" N ASN B3127 " pdb=" CA ASN B3127 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.18e-02 7.18e+03 6.53e+00 bond pdb=" N ARG B3123 " pdb=" CA ARG B3123 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.21e+00 bond pdb=" N THR B1271 " pdb=" CA THR B1271 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.80e+00 bond pdb=" N HIS B3126 " pdb=" CA HIS B3126 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.36e-02 5.41e+03 5.77e+00 ... (remaining 12077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 16029 2.54 - 5.08: 332 5.08 - 7.62: 15 7.62 - 10.17: 5 10.17 - 12.71: 3 Bond angle restraints: 16384 Sorted by residual: angle pdb=" N ASP B3871 " pdb=" CA ASP B3871 " pdb=" C ASP B3871 " ideal model delta sigma weight residual 111.17 102.94 8.23 1.41e+00 5.03e-01 3.41e+01 angle pdb=" N GLY B3872 " pdb=" CA GLY B3872 " pdb=" C GLY B3872 " ideal model delta sigma weight residual 110.97 118.94 -7.97 1.56e+00 4.11e-01 2.61e+01 angle pdb=" C5 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sigma weight residual 111.70 98.99 12.71 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C2 A2G B4706 " pdb=" C1 A2G B4706 " pdb=" O5 A2G B4706 " ideal model delta sigma weight residual 111.38 123.76 -12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" CA ARG B3150 " pdb=" C ARG B3150 " pdb=" O ARG B3150 " ideal model delta sigma weight residual 121.78 117.48 4.30 1.12e+00 7.97e-01 1.48e+01 ... (remaining 16379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 7128 22.38 - 44.76: 528 44.76 - 67.14: 106 67.14 - 89.52: 52 89.52 - 111.90: 21 Dihedral angle restraints: 7835 sinusoidal: 3661 harmonic: 4174 Sorted by residual: dihedral pdb=" CB CYS B3844 " pdb=" SG CYS B3844 " pdb=" SG CYS B3856 " pdb=" CB CYS B3856 " ideal model delta sinusoidal sigma weight residual 93.00 -176.69 -90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B3534 " pdb=" SG CYS B3534 " pdb=" SG CYS B3550 " pdb=" CB CYS B3550 " ideal model delta sinusoidal sigma weight residual 93.00 175.73 -82.73 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS B3701 " pdb=" SG CYS B3701 " pdb=" SG CYS B3716 " pdb=" CB CYS B3716 " ideal model delta sinusoidal sigma weight residual 93.00 169.67 -76.67 1 1.00e+01 1.00e-02 7.39e+01 ... (remaining 7832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1583 0.081 - 0.161: 181 0.161 - 0.242: 9 0.242 - 0.322: 2 0.322 - 0.403: 2 Chirality restraints: 1777 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B3317 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C2 A2G B4703 " pdb=" C1 A2G B4703 " pdb=" C3 A2G B4703 " pdb=" N2 A2G B4703 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B3259 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1774 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.292 2.00e-02 2.50e+03 2.48e-01 7.70e+02 pdb=" C7 NAG I 1 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.278 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" C7 NAG E 2 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.402 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.274 2.00e-02 2.50e+03 2.32e-01 6.72e+02 pdb=" C7 NAG H 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.016 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 488 2.70 - 3.25: 12139 3.25 - 3.80: 18452 3.80 - 4.35: 24350 4.35 - 4.90: 39380 Nonbonded interactions: 94809 Sorted by model distance: nonbonded pdb=" OD2 ASP B3746 " pdb="CA CA B4723 " model vdw 2.145 3.250 nonbonded pdb=" OD2 ASP B3626 " pdb="CA CA B4720 " model vdw 2.161 3.250 nonbonded pdb=" OE2 GLU B3753 " pdb="CA CA B4723 " model vdw 2.166 3.250 nonbonded pdb=" OD1 ASP B3616 " pdb="CA CA B4720 " model vdw 2.188 3.250 nonbonded pdb=" OD2 ASP B3585 " pdb="CA CA B4719 " model vdw 2.199 3.250 ... (remaining 94804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 1.430 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.008 0.542 12178 Z= 0.728 Angle : 0.827 12.707 16593 Z= 0.423 Chirality : 0.051 0.403 1777 Planarity : 0.013 0.248 2163 Dihedral : 17.918 111.900 4953 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer: Outliers : 2.26 % Allowed : 17.50 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.22), residues: 1432 helix: -3.26 (0.78), residues: 26 sheet: -0.69 (0.30), residues: 276 loop : -0.65 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B3635 TYR 0.013 0.001 TYR B3202 PHE 0.016 0.001 PHE B3000 TRP 0.011 0.001 TRP B3531 HIS 0.004 0.001 HIS B3732 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.22 (12082) covalent geometry : angle 0.80220 / 0.42 (16384) SS BOND : bond 0.00234 / 0.16 ( 64) SS BOND : angle 0.83442 / 0.56 ( 128) hydrogen bonds : bond 0.24352 / 15.99 ( 251) hydrogen bonds : angle 10.13296 / 6.76 ( 546) Misc. bond : bond 0.34167 / 20.09 ( 5) link_ALPHA1-3 : bond 0.00234 / 0.17 ( 3) link_ALPHA1-3 : angle 1.05516 / 0.67 ( 9) link_ALPHA1-6 : bond 0.00738 / 0.38 ( 3) link_ALPHA1-6 : angle 0.82468 / 0.39 ( 9) link_BETA1-4 : bond 0.00631 / 0.35 ( 12) link_BETA1-4 : angle 2.42633 / 1.56 ( 36) link_NAG-ASN : bond 0.00639 / 0.40 ( 9) link_NAG-ASN : angle 4.24648 / 2.73 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4108 LEU cc_start: 0.8017 (mp) cc_final: 0.7604 (mp) REVERT: A 4165 SER cc_start: 0.6779 (m) cc_final: 0.5965 (p) REVERT: A 4187 ASP cc_start: 0.8184 (t0) cc_final: 0.7903 (t0) REVERT: B 3148 ASP cc_start: 0.4267 (p0) cc_final: 0.4050 (p0) REVERT: B 3308 MET cc_start: 0.8246 (mtm) cc_final: 0.8014 (ttm) REVERT: B 3683 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7337 (m-70) REVERT: B 3755 ASN cc_start: 0.7769 (t0) cc_final: 0.7552 (t0) REVERT: B 3791 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8297 (p0) REVERT: B 3897 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6364 (ppp80) outliers start: 29 outliers final: 15 residues processed: 99 average time/residue: 0.1132 time to fit residues: 16.4276 Evaluate side-chains 81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4194 VAL Chi-restraints excluded: chain A residue 4313 VAL Chi-restraints excluded: chain A residue 4359 SER Chi-restraints excluded: chain A residue 4412 CYS Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3131 THR Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3373 THR Chi-restraints excluded: chain B residue 3408 SER Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3791 ASP Chi-restraints excluded: chain B residue 3844 CYS Chi-restraints excluded: chain B residue 3897 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B3057 ASN B3066 GLN B3105 ASN ** B3207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3602 GLN B3733 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147280 restraints weight = 23224.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145740 restraints weight = 39569.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143741 restraints weight = 37791.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142787 restraints weight = 31238.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140463 restraints weight = 33019.576| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12178 Z= 0.148 Angle : 0.697 10.050 16593 Z= 0.347 Chirality : 0.049 0.329 1777 Planarity : 0.004 0.053 2163 Dihedral : 12.347 91.227 2243 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.19 % Allowed : 16.41 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1432 helix: -2.22 (1.16), residues: 20 sheet: -0.28 (0.32), residues: 260 loop : -0.72 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B3238 TYR 0.014 0.002 TYR B3244 PHE 0.012 0.001 PHE B3322 TRP 0.012 0.001 TRP A4160 HIS 0.005 0.001 HIS A4387 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (12082) covalent geometry : angle 0.67181 / 0.34 (16384) SS BOND : bond 0.00279 / 0.20 ( 64) SS BOND : angle 0.75145 / 0.51 ( 128) hydrogen bonds : bond 0.04659 / 3.03 ( 251) hydrogen bonds : angle 7.42329 / 4.82 ( 546) Misc. bond : bond 0.00378 / 0.23 ( 5) link_ALPHA1-3 : bond 0.00664 / 0.45 ( 3) link_ALPHA1-3 : angle 2.08791 / 1.14 ( 9) link_ALPHA1-6 : bond 0.00683 / 0.45 ( 3) link_ALPHA1-6 : angle 1.89126 / 0.97 ( 9) link_BETA1-4 : bond 0.00680 / 0.45 ( 12) link_BETA1-4 : angle 2.71059 / 1.89 ( 36) link_NAG-ASN : bond 0.00610 / 0.38 ( 9) link_NAG-ASN : angle 3.15391 / 1.89 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 66 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4090 ASP cc_start: 0.0527 (OUTLIER) cc_final: 0.0059 (m-30) REVERT: B 3683 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7218 (m-70) REVERT: B 3752 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7468 (p0) REVERT: B 3897 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6712 (ppp80) REVERT: B 3906 ASN cc_start: 0.7000 (p0) cc_final: 0.5199 (m110) outliers start: 41 outliers final: 18 residues processed: 103 average time/residue: 0.1193 time to fit residues: 17.7121 Evaluate side-chains 80 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4090 ASP Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4172 THR Chi-restraints excluded: chain A residue 4359 SER Chi-restraints excluded: chain A residue 4412 CYS Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 2933 CYS Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3105 ASN Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3373 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3791 ASP Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Chi-restraints excluded: chain B residue 3897 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 48 optimal weight: 0.0980 chunk 35 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B3722 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 = 0.4277 r_free = 0.4277 target = 0.175590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144957 restraints weight = 23361.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143466 restraints weight = 38305.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141556 restraints weight = 29028.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139350 restraints weight = 34668.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138042 restraints weight = 34348.341| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12178 Z= 0.199 Angle : 0.697 10.057 16593 Z= 0.347 Chirality : 0.049 0.188 1777 Planarity : 0.004 0.045 2163 Dihedral : 11.319 88.918 2234 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.73 % Allowed : 16.33 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1432 helix: -2.60 (0.87), residues: 32 sheet: -0.35 (0.32), residues: 267 loop : -0.82 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2961 TYR 0.015 0.002 TYR B3244 PHE 0.020 0.002 PHE B3393 TRP 0.012 0.001 TRP A4160 HIS 0.006 0.001 HIS B3331 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (12082) covalent geometry : angle 0.67538 / 0.34 (16384) SS BOND : bond 0.00300 / 0.23 ( 64) SS BOND : angle 0.82258 / 0.57 ( 128) hydrogen bonds : bond 0.03920 / 2.55 ( 251) hydrogen bonds : angle 7.00200 / 4.57 ( 546) Misc. bond : bond 0.00130 / 0.09 ( 5) link_ALPHA1-3 : bond 0.00880 / 0.60 ( 3) link_ALPHA1-3 : angle 1.49199 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00746 / 0.47 ( 3) link_ALPHA1-6 : angle 1.95201 / 1.08 ( 9) link_BETA1-4 : bond 0.00492 / 0.34 ( 12) link_BETA1-4 : angle 2.68156 / 1.86 ( 36) link_NAG-ASN : bond 0.00468 / 0.24 ( 9) link_NAG-ASN : angle 2.68197 / 1.54 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 60 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4090 ASP cc_start: 0.0338 (OUTLIER) cc_final: -0.0167 (m-30) REVERT: B 3452 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8503 (mttt) REVERT: B 3683 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7291 (m-70) REVERT: B 3708 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6677 (mmt180) REVERT: B 3752 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7484 (p0) REVERT: B 3797 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7032 (mpt) REVERT: B 3897 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6688 (ppp80) REVERT: B 3906 ASN cc_start: 0.7182 (p0) cc_final: 0.5483 (m-40) outliers start: 48 outliers final: 24 residues processed: 102 average time/residue: 0.1157 time to fit residues: 17.2392 Evaluate side-chains 87 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4090 ASP Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER Chi-restraints excluded: chain A residue 4172 THR Chi-restraints excluded: chain A residue 4246 VAL Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3148 ASP Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3271 LEU Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3708 ARG Chi-restraints excluded: chain B residue 3744 THR Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3791 ASP Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Chi-restraints excluded: chain B residue 3897 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B3789 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.175821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145015 restraints weight = 23249.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.140658 restraints weight = 37856.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137930 restraints weight = 39095.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137529 restraints weight = 35426.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135923 restraints weight = 30952.586| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12178 Z= 0.162 Angle : 0.659 10.022 16593 Z= 0.326 Chirality : 0.048 0.189 1777 Planarity : 0.004 0.045 2163 Dihedral : 10.038 80.006 2230 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.42 % Allowed : 17.50 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1432 helix: -1.96 (0.98), residues: 32 sheet: -0.37 (0.32), residues: 269 loop : -0.83 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2961 TYR 0.014 0.002 TYR A4287 PHE 0.016 0.001 PHE B3393 TRP 0.012 0.001 TRP A4160 HIS 0.004 0.001 HIS B3331 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (12082) covalent geometry : angle 0.63825 / 0.32 (16384) SS BOND : bond 0.00258 / 0.18 ( 64) SS BOND : angle 0.81221 / 0.56 ( 128) hydrogen bonds : bond 0.03373 / 2.17 ( 251) hydrogen bonds : angle 6.68959 / 4.36 ( 546) Misc. bond : bond 0.00161 / 0.10 ( 5) link_ALPHA1-3 : bond 0.00895 / 0.59 ( 3) link_ALPHA1-3 : angle 1.61703 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00681 / 0.42 ( 3) link_ALPHA1-6 : angle 1.99462 / 1.13 ( 9) link_BETA1-4 : bond 0.00506 / 0.34 ( 12) link_BETA1-4 : angle 2.52155 / 1.76 ( 36) link_NAG-ASN : bond 0.00382 / 0.19 ( 9) link_NAG-ASN : angle 2.41482 / 1.43 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 59 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4090 ASP cc_start: 0.0260 (OUTLIER) cc_final: -0.0202 (m-30) REVERT: B 3683 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7322 (m-70) REVERT: B 3752 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7714 (p0) REVERT: B 3753 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: B 3789 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.7838 (t0) REVERT: B 3791 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8501 (p0) REVERT: B 3797 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6881 (mpt) REVERT: B 3897 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6617 (ppp80) REVERT: B 3906 ASN cc_start: 0.6606 (p0) cc_final: 0.4852 (m110) outliers start: 44 outliers final: 23 residues processed: 98 average time/residue: 0.1012 time to fit residues: 15.2092 Evaluate side-chains 84 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4090 ASP Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3232 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3373 THR Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3753 GLU Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3789 ASN Chi-restraints excluded: chain B residue 3791 ASP Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Chi-restraints excluded: chain B residue 3897 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 39 optimal weight: 0.0370 chunk 128 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4234 ASN ** B3921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.176502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145809 restraints weight = 23313.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.141910 restraints weight = 38185.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138164 restraints weight = 36173.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138130 restraints weight = 35484.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136548 restraints weight = 30908.437| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12178 Z= 0.137 Angle : 0.638 10.030 16593 Z= 0.315 Chirality : 0.047 0.188 1777 Planarity : 0.004 0.050 2163 Dihedral : 9.132 65.745 2230 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.95 % Allowed : 18.27 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1432 helix: -1.86 (0.98), residues: 32 sheet: -0.39 (0.33), residues: 256 loop : -0.83 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3793 TYR 0.014 0.001 TYR A4287 PHE 0.013 0.001 PHE B3393 TRP 0.011 0.001 TRP A4160 HIS 0.004 0.001 HIS B3732 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12082) covalent geometry : angle 0.61880 / 0.31 (16384) SS BOND : bond 0.00268 / 0.18 ( 64) SS BOND : angle 0.73477 / 0.50 ( 128) hydrogen bonds : bond 0.03192 / 2.04 ( 251) hydrogen bonds : angle 6.52077 / 4.24 ( 546) Misc. bond : bond 0.00273 / 0.15 ( 5) link_ALPHA1-3 : bond 0.00934 / 0.60 ( 3) link_ALPHA1-3 : angle 1.59056 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00700 / 0.42 ( 3) link_ALPHA1-6 : angle 1.96985 / 1.14 ( 9) link_BETA1-4 : bond 0.00509 / 0.34 ( 12) link_BETA1-4 : angle 2.40332 / 1.68 ( 36) link_NAG-ASN : bond 0.00354 / 0.17 ( 9) link_NAG-ASN : angle 2.25191 / 1.33 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 57 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3683 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7304 (m-70) REVERT: B 3752 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7868 (p0) REVERT: B 3753 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: B 3791 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8549 (p0) REVERT: B 3797 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6723 (mpt) REVERT: B 3897 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6872 (ppp80) REVERT: B 3906 ASN cc_start: 0.6506 (p0) cc_final: 0.4732 (m-40) outliers start: 38 outliers final: 23 residues processed: 91 average time/residue: 0.1167 time to fit residues: 15.5124 Evaluate side-chains 82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 2933 CYS Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3753 GLU Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3791 ASP Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Chi-restraints excluded: chain B residue 3897 ARG Chi-restraints excluded: chain B residue 3921 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 113 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 33 optimal weight: 50.0000 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B3921 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 = 0.4291 r_free = 0.4291 target = 0.176508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147023 restraints weight = 23511.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142011 restraints weight = 35256.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138787 restraints weight = 34185.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137966 restraints weight = 36470.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136474 restraints weight = 35448.845| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12178 Z= 0.130 Angle : 0.624 10.001 16593 Z= 0.308 Chirality : 0.047 0.194 1777 Planarity : 0.004 0.054 2163 Dihedral : 7.971 54.779 2230 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.11 % Allowed : 18.82 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1432 helix: -1.67 (1.01), residues: 32 sheet: -0.40 (0.33), residues: 258 loop : -0.79 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B3083 TYR 0.013 0.001 TYR A4287 PHE 0.020 0.001 PHE B3135 TRP 0.011 0.001 TRP A4160 HIS 0.003 0.001 HIS B3732 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (12082) covalent geometry : angle 0.60644 / 0.30 (16384) SS BOND : bond 0.00229 / 0.16 ( 64) SS BOND : angle 0.71612 / 0.49 ( 128) hydrogen bonds : bond 0.03012 / 1.92 ( 251) hydrogen bonds : angle 6.36422 / 4.13 ( 546) Misc. bond : bond 0.00171 / 0.10 ( 5) link_ALPHA1-3 : bond 0.01004 / 0.65 ( 3) link_ALPHA1-3 : angle 1.51389 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00840 / 0.52 ( 3) link_ALPHA1-6 : angle 2.41264 / 1.52 ( 9) link_BETA1-4 : bond 0.00486 / 0.33 ( 12) link_BETA1-4 : angle 2.21001 / 1.51 ( 36) link_NAG-ASN : bond 0.00325 / 0.16 ( 9) link_NAG-ASN : angle 2.16001 / 1.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3100 ASP cc_start: 0.4965 (t0) cc_final: 0.4676 (t0) REVERT: B 3452 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8626 (mttt) REVERT: B 3683 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7227 (m-70) REVERT: B 3752 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7905 (p0) REVERT: B 3753 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6707 (mm-30) REVERT: B 3791 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8516 (p0) REVERT: B 3906 ASN cc_start: 0.6459 (p0) cc_final: 0.4482 (m-40) outliers start: 40 outliers final: 27 residues processed: 94 average time/residue: 0.1060 time to fit residues: 14.9630 Evaluate side-chains 89 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3002 CYS Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3744 THR Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3753 GLU Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3791 ASP Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3855 VAL Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Chi-restraints excluded: chain B residue 3921 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 142 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 7 optimal weight: 40.0000 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4166 GLN B2903 HIS B2931 ASN B3088 HIS B3722 HIS B3789 ASN ** B3921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.175015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143537 restraints weight = 23333.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140315 restraints weight = 40715.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137181 restraints weight = 40338.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136847 restraints weight = 32753.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135169 restraints weight = 29573.449| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12178 Z= 0.183 Angle : 0.656 10.397 16593 Z= 0.324 Chirality : 0.048 0.209 1777 Planarity : 0.004 0.055 2163 Dihedral : 7.740 54.084 2226 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.73 % Allowed : 18.90 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1432 helix: -1.53 (1.03), residues: 32 sheet: -0.37 (0.33), residues: 258 loop : -0.85 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3150 TYR 0.013 0.002 TYR B3221 PHE 0.019 0.001 PHE B3393 TRP 0.010 0.001 TRP B3531 HIS 0.008 0.001 HIS B3088 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (12082) covalent geometry : angle 0.63946 / 0.32 (16384) SS BOND : bond 0.00279 / 0.18 ( 64) SS BOND : angle 0.78444 / 0.55 ( 128) hydrogen bonds : bond 0.03189 / 2.03 ( 251) hydrogen bonds : angle 6.42348 / 4.20 ( 546) Misc. bond : bond 0.00148 / 0.09 ( 5) link_ALPHA1-3 : bond 0.00966 / 0.64 ( 3) link_ALPHA1-3 : angle 1.54572 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00721 / 0.46 ( 3) link_ALPHA1-6 : angle 2.25142 / 1.33 ( 9) link_BETA1-4 : bond 0.00473 / 0.32 ( 12) link_BETA1-4 : angle 2.12062 / 1.42 ( 36) link_NAG-ASN : bond 0.00371 / 0.18 ( 9) link_NAG-ASN : angle 2.13438 / 1.25 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 57 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4160 TRP cc_start: 0.7389 (p90) cc_final: 0.7015 (p90) REVERT: A 4169 GLU cc_start: 0.6206 (mm-30) cc_final: 0.5967 (mm-30) REVERT: B 3683 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7217 (m-70) REVERT: B 3708 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6622 (mmt180) REVERT: B 3712 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.6960 (p0) REVERT: B 3726 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: B 3752 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7821 (p0) REVERT: B 3753 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6832 (mm-30) REVERT: B 3789 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.7918 (t0) outliers start: 48 outliers final: 31 residues processed: 98 average time/residue: 0.1099 time to fit residues: 15.9505 Evaluate side-chains 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 52 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4166 GLN Chi-restraints excluded: chain A residue 4170 VAL Chi-restraints excluded: chain A residue 4183 THR Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3002 CYS Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3232 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3408 SER Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3708 ARG Chi-restraints excluded: chain B residue 3712 ASP Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3744 THR Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3753 GLU Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3789 ASN Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3855 VAL Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 26 optimal weight: 40.0000 chunk 32 optimal weight: 0.0000 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.176147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145538 restraints weight = 23482.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.142513 restraints weight = 38408.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.139426 restraints weight = 37802.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138227 restraints weight = 35466.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136399 restraints weight = 31742.137| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12178 Z= 0.129 Angle : 0.640 11.166 16593 Z= 0.316 Chirality : 0.047 0.204 1777 Planarity : 0.004 0.062 2163 Dihedral : 7.239 54.868 2224 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.64 % Allowed : 19.83 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1432 helix: -1.45 (1.04), residues: 32 sheet: -0.41 (0.33), residues: 253 loop : -0.78 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B3507 TYR 0.013 0.001 TYR A4287 PHE 0.013 0.001 PHE B3297 TRP 0.012 0.001 TRP A4160 HIS 0.004 0.001 HIS B3732 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (12082) covalent geometry : angle 0.62477 / 0.31 (16384) SS BOND : bond 0.00211 / 0.14 ( 64) SS BOND : angle 0.74078 / 0.52 ( 128) hydrogen bonds : bond 0.03044 / 1.93 ( 251) hydrogen bonds : angle 6.25726 / 4.06 ( 546) Misc. bond : bond 0.00347 / 0.18 ( 5) link_ALPHA1-3 : bond 0.00994 / 0.64 ( 3) link_ALPHA1-3 : angle 1.43911 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00714 / 0.43 ( 3) link_ALPHA1-6 : angle 2.15754 / 1.29 ( 9) link_BETA1-4 : bond 0.00490 / 0.33 ( 12) link_BETA1-4 : angle 1.94744 / 1.29 ( 36) link_NAG-ASN : bond 0.00330 / 0.16 ( 9) link_NAG-ASN : angle 2.15932 / 1.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 57 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3413 PHE cc_start: 0.8413 (t80) cc_final: 0.8158 (t80) REVERT: B 3683 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7288 (m-70) REVERT: B 3712 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.6952 (p0) REVERT: B 3752 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7871 (p0) REVERT: B 3753 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6599 (mm-30) REVERT: B 3897 ARG cc_start: 0.5606 (OUTLIER) cc_final: 0.5353 (tmm-80) outliers start: 34 outliers final: 27 residues processed: 86 average time/residue: 0.1044 time to fit residues: 13.7349 Evaluate side-chains 89 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3002 CYS Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3232 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3712 ASP Chi-restraints excluded: chain B residue 3744 THR Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3753 GLU Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3855 VAL Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Chi-restraints excluded: chain B residue 3897 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 50.0000 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.175793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144793 restraints weight = 23211.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142065 restraints weight = 38202.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137783 restraints weight = 37625.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136887 restraints weight = 37155.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135289 restraints weight = 32046.315| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12178 Z= 0.148 Angle : 0.637 10.006 16593 Z= 0.316 Chirality : 0.047 0.208 1777 Planarity : 0.004 0.056 2163 Dihedral : 6.978 54.902 2224 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.64 % Allowed : 19.91 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1432 helix: -1.15 (1.16), residues: 26 sheet: -0.35 (0.33), residues: 250 loop : -0.80 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3897 TYR 0.013 0.001 TYR A4287 PHE 0.014 0.001 PHE B3393 TRP 0.009 0.001 TRP B3531 HIS 0.004 0.001 HIS B3732 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (12082) covalent geometry : angle 0.62226 / 0.31 (16384) SS BOND : bond 0.00222 / 0.16 ( 64) SS BOND : angle 0.73214 / 0.51 ( 128) hydrogen bonds : bond 0.02965 / 1.90 ( 251) hydrogen bonds : angle 6.18534 / 4.02 ( 546) Misc. bond : bond 0.00249 / 0.13 ( 5) link_ALPHA1-3 : bond 0.00957 / 0.63 ( 3) link_ALPHA1-3 : angle 1.41203 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00692 / 0.42 ( 3) link_ALPHA1-6 : angle 2.10191 / 1.24 ( 9) link_BETA1-4 : bond 0.00480 / 0.32 ( 12) link_BETA1-4 : angle 1.88993 / 1.23 ( 36) link_NAG-ASN : bond 0.00316 / 0.16 ( 9) link_NAG-ASN : angle 2.16704 / 1.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 56 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3683 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7289 (m-70) REVERT: B 3712 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.6974 (p0) REVERT: B 3752 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7902 (p0) REVERT: B 3753 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6792 (mm-30) outliers start: 34 outliers final: 28 residues processed: 86 average time/residue: 0.1014 time to fit residues: 13.4811 Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4166 GLN Chi-restraints excluded: chain A residue 4172 THR Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3002 CYS Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3232 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3348 ILE Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3712 ASP Chi-restraints excluded: chain B residue 3744 THR Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3753 GLU Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3855 VAL Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 69 optimal weight: 0.0060 chunk 142 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.176166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146219 restraints weight = 23431.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141261 restraints weight = 37620.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138479 restraints weight = 38278.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138142 restraints weight = 39208.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137827 restraints weight = 28486.128| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12178 Z= 0.129 Angle : 0.624 10.055 16593 Z= 0.309 Chirality : 0.047 0.230 1777 Planarity : 0.004 0.056 2163 Dihedral : 6.843 55.405 2224 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.57 % Allowed : 19.98 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.22), residues: 1432 helix: -1.12 (1.16), residues: 26 sheet: -0.27 (0.32), residues: 264 loop : -0.77 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A4167 TYR 0.013 0.001 TYR A4287 PHE 0.011 0.001 PHE B3393 TRP 0.010 0.001 TRP B3531 HIS 0.004 0.001 HIS B3732 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12082) covalent geometry : angle 0.60973 / 0.31 (16384) SS BOND : bond 0.00200 / 0.14 ( 64) SS BOND : angle 0.69618 / 0.48 ( 128) hydrogen bonds : bond 0.02895 / 1.86 ( 251) hydrogen bonds : angle 6.13899 / 3.99 ( 546) Misc. bond : bond 0.00229 / 0.12 ( 5) link_ALPHA1-3 : bond 0.00931 / 0.61 ( 3) link_ALPHA1-3 : angle 1.40333 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00652 / 0.39 ( 3) link_ALPHA1-6 : angle 2.02117 / 1.20 ( 9) link_BETA1-4 : bond 0.00488 / 0.33 ( 12) link_BETA1-4 : angle 1.82008 / 1.18 ( 36) link_NAG-ASN : bond 0.00315 / 0.16 ( 9) link_NAG-ASN : angle 2.15461 / 1.27 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3341 ASP cc_start: 0.8282 (t0) cc_final: 0.7936 (t0) REVERT: B 3462 TYR cc_start: 0.9160 (m-10) cc_final: 0.8854 (m-10) REVERT: B 3683 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7336 (m-70) REVERT: B 3712 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7115 (p0) REVERT: B 3752 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7898 (p0) REVERT: B 3753 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6733 (mm-30) REVERT: B 3906 ASN cc_start: 0.6376 (p0) cc_final: 0.4488 (m-40) outliers start: 33 outliers final: 29 residues processed: 85 average time/residue: 0.0958 time to fit residues: 12.7440 Evaluate side-chains 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4166 GLN Chi-restraints excluded: chain A residue 4172 THR Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3002 CYS Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3232 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3408 SER Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3712 ASP Chi-restraints excluded: chain B residue 3744 THR Chi-restraints excluded: chain B residue 3752 ASP Chi-restraints excluded: chain B residue 3753 GLU Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3822 ARG Chi-restraints excluded: chain B residue 3855 VAL Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 50.0000 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 138 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A4166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.174511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144029 restraints weight = 23312.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140440 restraints weight = 38328.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136629 restraints weight = 40028.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135750 restraints weight = 39723.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134272 restraints weight = 33345.587| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12178 Z= 0.204 Angle : 0.664 10.361 16593 Z= 0.330 Chirality : 0.048 0.217 1777 Planarity : 0.004 0.057 2163 Dihedral : 7.027 54.836 2224 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 2.80 % Allowed : 19.91 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1432 helix: -1.05 (1.20), residues: 26 sheet: -0.38 (0.32), residues: 264 loop : -0.86 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A4167 TYR 0.014 0.002 TYR B3136 PHE 0.046 0.002 PHE B3413 TRP 0.019 0.002 TRP A4160 HIS 0.004 0.001 HIS B1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (12082) covalent geometry : angle 0.64985 / 0.33 (16384) SS BOND : bond 0.00267 / 0.19 ( 64) SS BOND : angle 0.79565 / 0.56 ( 128) hydrogen bonds : bond 0.03090 / 1.97 ( 251) hydrogen bonds : angle 6.26194 / 4.10 ( 546) Misc. bond : bond 0.00217 / 0.11 ( 5) link_ALPHA1-3 : bond 0.00910 / 0.62 ( 3) link_ALPHA1-3 : angle 1.46797 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00679 / 0.44 ( 3) link_ALPHA1-6 : angle 2.15754 / 1.26 ( 9) link_BETA1-4 : bond 0.00473 / 0.32 ( 12) link_BETA1-4 : angle 1.90724 / 1.21 ( 36) link_NAG-ASN : bond 0.00349 / 0.18 ( 9) link_NAG-ASN : angle 2.19302 / 1.28 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.41 seconds wall clock time: 32 minutes 47.24 seconds (1967.24 seconds total)