Starting phenix.real_space_refine on Sat Aug 23 12:34:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx9_36693/08_2025/8jx9_36693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx9_36693/08_2025/8jx9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jx9_36693/08_2025/8jx9_36693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx9_36693/08_2025/8jx9_36693.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx9_36693/08_2025/8jx9_36693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx9_36693/08_2025/8jx9_36693.cif" } 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-2.0-5787/lib/python3.9/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, 118 Unusual residues: {' CA': 20, 'A2G': 5, 'NAG': 2} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.99, per 1000 atoms: 0.25 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: 0.94 Conformation dependent library (CDL) restraints added in 580.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 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: 0.42 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: 2.19 Time building geometry restraints manager: 1.16 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 2.510 nonbonded pdb=" OD2 ASP B3626 " pdb="CA CA B4720 " model vdw 2.161 2.510 nonbonded pdb=" OE2 GLU B3753 " pdb="CA CA B4723 " model vdw 2.166 2.510 nonbonded pdb=" OD1 ASP B3616 " pdb="CA CA B4720 " model vdw 2.188 2.510 nonbonded pdb=" OD2 ASP B3585 " pdb="CA CA B4719 " model vdw 2.199 2.510 ... (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: 1.250 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 11.960 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 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 aren 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 covalent geometry : bond 0.00425 (12082) covalent geometry : angle 0.80220 (16384) SS BOND : bond 0.00234 ( 64) SS BOND : angle 0.83442 ( 128) hydrogen bonds : bond 0.24352 ( 251) hydrogen bonds : angle 10.13296 ( 546) Misc. bond : bond 0.34167 ( 5) link_ALPHA1-3 : bond 0.00234 ( 3) link_ALPHA1-3 : angle 1.05516 ( 9) link_ALPHA1-6 : bond 0.00738 ( 3) link_ALPHA1-6 : angle 0.82468 ( 9) link_BETA1-4 : bond 0.00631 ( 12) link_BETA1-4 : angle 2.42633 ( 36) link_NAG-ASN : bond 0.00639 ( 9) link_NAG-ASN : angle 4.24648 ( 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 : 0.474 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: 0.1123 time to fit residues: 16.1771 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 : 0.394 ------------------------------------------------------------------------------- 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: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4293 r_free = 0.4293 target = 0.176864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.150081 restraints weight = 23313.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147138 restraints weight = 42083.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144925 restraints weight = 36532.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143115 restraints weight = 36043.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141535 restraints weight = 37532.164| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12178 Z= 0.145 Angle : 0.689 9.863 16593 Z= 0.341 Chirality : 0.048 0.252 1777 Planarity : 0.004 0.056 2163 Dihedral : 12.448 91.588 2243 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.03 % Allowed : 16.41 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.22), residues: 1432 helix: -2.17 (1.16), residues: 20 sheet: -0.30 (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 A4176 TYR 0.013 0.002 TYR A4287 PHE 0.012 0.001 PHE B3393 TRP 0.010 0.001 TRP A4160 HIS 0.004 0.001 HIS B3331 Details of bonding type rmsd covalent geometry : bond 0.00325 (12082) covalent geometry : angle 0.66170 (16384) SS BOND : bond 0.00258 ( 64) SS BOND : angle 0.72068 ( 128) hydrogen bonds : bond 0.04494 ( 251) hydrogen bonds : angle 7.46445 ( 546) Misc. bond : bond 0.00134 ( 5) link_ALPHA1-3 : bond 0.00618 ( 3) link_ALPHA1-3 : angle 2.20955 ( 9) link_ALPHA1-6 : bond 0.00555 ( 3) link_ALPHA1-6 : angle 1.90621 ( 9) link_BETA1-4 : bond 0.00619 ( 12) link_BETA1-4 : angle 2.81824 ( 36) link_NAG-ASN : bond 0.00590 ( 9) link_NAG-ASN : angle 3.18612 ( 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: 39 poor density : 68 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3123 ARG cc_start: 0.6790 (ptp-110) cc_final: 0.6480 (ptp-110) REVERT: B 3683 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7221 (m-70) REVERT: B 3897 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6710 (ppp80) outliers start: 39 outliers final: 17 residues processed: 102 average time/residue: 0.1093 time to fit residues: 16.3035 Evaluate side-chains 76 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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 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 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: 0.0050 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 40.0000 chunk 112 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 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: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B3722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3755 ASN B3789 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.172928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152766 restraints weight = 23759.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151743 restraints weight = 57222.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.150143 restraints weight = 21556.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.150195 restraints weight = 17591.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.150252 restraints weight = 10066.985| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12178 Z= 0.317 Angle : 0.801 10.640 16593 Z= 0.399 Chirality : 0.053 0.210 1777 Planarity : 0.005 0.046 2163 Dihedral : 12.083 93.972 2233 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 4.12 % Allowed : 16.80 % 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 aren not related in a simple way. whole: -1.45 (0.21), residues: 1432 helix: -2.40 (0.90), residues: 32 sheet: -0.57 (0.31), residues: 271 loop : -1.09 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B2961 TYR 0.024 0.002 TYR B3244 PHE 0.034 0.002 PHE B3393 TRP 0.014 0.002 TRP B3339 HIS 0.010 0.002 HIS B3331 Details of bonding type rmsd covalent geometry : bond 0.00733 (12082) covalent geometry : angle 0.77754 (16384) SS BOND : bond 0.00450 ( 64) SS BOND : angle 1.06345 ( 128) hydrogen bonds : bond 0.04420 ( 251) hydrogen bonds : angle 7.30799 ( 546) Misc. bond : bond 0.00254 ( 5) link_ALPHA1-3 : bond 0.00863 ( 3) link_ALPHA1-3 : angle 1.46928 ( 9) link_ALPHA1-6 : bond 0.00693 ( 3) link_ALPHA1-6 : angle 2.03405 ( 9) link_BETA1-4 : bond 0.00553 ( 12) link_BETA1-4 : angle 2.88209 ( 36) link_NAG-ASN : bond 0.00612 ( 9) link_NAG-ASN : angle 2.91877 ( 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 112 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 59 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2938 ASP cc_start: 0.0893 (OUTLIER) cc_final: 0.0608 (p0) REVERT: B 3092 MET cc_start: 0.4681 (mpt) cc_final: 0.4472 (mpt) REVERT: B 3683 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7152 (m-70) REVERT: B 3726 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: B 3789 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8014 (t0) outliers start: 53 outliers final: 29 residues processed: 106 average time/residue: 0.1011 time to fit residues: 16.0496 Evaluate side-chains 92 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 2938 ASP 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 3131 THR Chi-restraints excluded: chain B residue 3148 ASP 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 3271 LEU Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3373 THR Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3509 LEU Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3515 SER Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3726 ASP Chi-restraints excluded: chain B residue 3744 THR 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 3855 VAL Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 66 optimal weight: 0.4980 chunk 6 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.175399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147015 restraints weight = 23339.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139946 restraints weight = 35150.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138178 restraints weight = 40335.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136847 restraints weight = 33392.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135924 restraints weight = 30608.200| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12178 Z= 0.137 Angle : 0.658 9.976 16593 Z= 0.325 Chirality : 0.047 0.193 1777 Planarity : 0.004 0.044 2163 Dihedral : 10.516 84.707 2228 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.33 % Allowed : 19.05 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.22), residues: 1432 helix: -1.75 (1.06), residues: 26 sheet: -0.45 (0.32), residues: 257 loop : -0.91 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B3793 TYR 0.014 0.001 TYR A4287 PHE 0.012 0.001 PHE B3393 TRP 0.012 0.001 TRP A4160 HIS 0.004 0.001 HIS B3732 Details of bonding type rmsd covalent geometry : bond 0.00309 (12082) covalent geometry : angle 0.63684 (16384) SS BOND : bond 0.00228 ( 64) SS BOND : angle 0.77301 ( 128) hydrogen bonds : bond 0.03359 ( 251) hydrogen bonds : angle 6.79875 ( 546) Misc. bond : bond 0.00166 ( 5) link_ALPHA1-3 : bond 0.00871 ( 3) link_ALPHA1-3 : angle 1.62148 ( 9) link_ALPHA1-6 : bond 0.00733 ( 3) link_ALPHA1-6 : angle 2.02726 ( 9) link_BETA1-4 : bond 0.00512 ( 12) link_BETA1-4 : angle 2.54430 ( 36) link_NAG-ASN : bond 0.00408 ( 9) link_NAG-ASN : angle 2.49868 ( 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 91 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2938 ASP cc_start: 0.0901 (OUTLIER) cc_final: 0.0639 (p0) REVERT: B 3683 HIS cc_start: 0.7682 (OUTLIER) cc_final: 0.7291 (m-70) REVERT: B 3708 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6372 (mmt-90) outliers start: 30 outliers final: 15 residues processed: 89 average time/residue: 0.1154 time to fit residues: 15.0896 Evaluate side-chains 72 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 2938 ASP Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3172 VAL 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 3478 CYS Chi-restraints excluded: chain B residue 3511 MET 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 3774 ILE Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 50.0000 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4234 ASN ** B3722 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 = 0.4275 r_free = 0.4275 target = 0.175291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144581 restraints weight = 23330.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141761 restraints weight = 39708.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138354 restraints weight = 40333.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137500 restraints weight = 39497.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135516 restraints weight = 33251.239| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1807 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= 0.145 Angle : 0.644 10.083 16593 Z= 0.316 Chirality : 0.047 0.203 1777 Planarity : 0.004 0.049 2163 Dihedral : 9.010 66.153 2226 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.88 % Allowed : 19.21 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.22), residues: 1432 helix: -1.42 (1.10), residues: 26 sheet: -0.42 (0.32), residues: 274 loop : -0.90 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B3897 TYR 0.014 0.001 TYR A4287 PHE 0.013 0.001 PHE B3393 TRP 0.012 0.001 TRP A4160 HIS 0.003 0.001 HIS B3732 Details of bonding type rmsd covalent geometry : bond 0.00329 (12082) covalent geometry : angle 0.62422 (16384) SS BOND : bond 0.00221 ( 64) SS BOND : angle 0.76718 ( 128) hydrogen bonds : bond 0.03229 ( 251) hydrogen bonds : angle 6.48498 ( 546) Misc. bond : bond 0.00254 ( 5) link_ALPHA1-3 : bond 0.00955 ( 3) link_ALPHA1-3 : angle 1.54477 ( 9) link_ALPHA1-6 : bond 0.00771 ( 3) link_ALPHA1-6 : angle 1.99520 ( 9) link_BETA1-4 : bond 0.00526 ( 12) link_BETA1-4 : angle 2.43019 ( 36) link_NAG-ASN : bond 0.00363 ( 9) link_NAG-ASN : angle 2.30642 ( 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 98 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4090 ASP cc_start: 0.1007 (OUTLIER) cc_final: 0.0800 (t70) REVERT: B 2938 ASP cc_start: 0.0525 (OUTLIER) cc_final: 0.0226 (p0) outliers start: 37 outliers final: 20 residues processed: 93 average time/residue: 0.1079 time to fit residues: 15.0003 Evaluate side-chains 77 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4090 ASP 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 2938 ASP Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3185 ILE 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 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 3644 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 113 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4166 GLN B1237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.175516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144573 restraints weight = 23551.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141366 restraints weight = 39892.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137965 restraints weight = 38030.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136979 restraints weight = 36957.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135400 restraints weight = 31536.997| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.1961 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= 0.144 Angle : 0.633 10.085 16593 Z= 0.312 Chirality : 0.047 0.226 1777 Planarity : 0.004 0.054 2163 Dihedral : 7.838 55.837 2222 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % 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 aren not related in a simple way. whole: -1.13 (0.22), residues: 1432 helix: -1.22 (1.13), residues: 26 sheet: -0.38 (0.33), residues: 259 loop : -0.88 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B3401 TYR 0.013 0.001 TYR B3136 PHE 0.020 0.001 PHE B3135 TRP 0.011 0.001 TRP A4160 HIS 0.006 0.001 HIS B3683 Details of bonding type rmsd covalent geometry : bond 0.00334 (12082) covalent geometry : angle 0.61294 (16384) SS BOND : bond 0.00215 ( 64) SS BOND : angle 0.75878 ( 128) hydrogen bonds : bond 0.03082 ( 251) hydrogen bonds : angle 6.38024 ( 546) Misc. bond : bond 0.00172 ( 5) link_ALPHA1-3 : bond 0.00967 ( 3) link_ALPHA1-3 : angle 1.54400 ( 9) link_ALPHA1-6 : bond 0.00783 ( 3) link_ALPHA1-6 : angle 2.37449 ( 9) link_BETA1-4 : bond 0.00487 ( 12) link_BETA1-4 : angle 2.21941 ( 36) link_NAG-ASN : bond 0.00371 ( 9) link_NAG-ASN : angle 2.46221 ( 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 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 86 average time/residue: 0.0977 time to fit residues: 13.1094 Evaluate side-chains 77 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4166 GLN 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 3172 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3348 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 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3707 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 142 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 100 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.176035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.148314 restraints weight = 23272.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145840 restraints weight = 42042.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143400 restraints weight = 43155.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142670 restraints weight = 41683.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.141134 restraints weight = 38670.946| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12178 Z= 0.116 Angle : 0.618 9.886 16593 Z= 0.304 Chirality : 0.047 0.257 1777 Planarity : 0.004 0.054 2163 Dihedral : 7.337 56.501 2222 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.57 % Allowed : 19.75 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.22), residues: 1432 helix: -1.20 (1.12), residues: 26 sheet: -0.29 (0.33), residues: 259 loop : -0.82 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B3150 TYR 0.013 0.001 TYR A4287 PHE 0.014 0.001 PHE B3135 TRP 0.010 0.001 TRP B3288 HIS 0.003 0.001 HIS B3732 Details of bonding type rmsd covalent geometry : bond 0.00262 (12082) covalent geometry : angle 0.60115 (16384) SS BOND : bond 0.00197 ( 64) SS BOND : angle 0.69836 ( 128) hydrogen bonds : bond 0.02969 ( 251) hydrogen bonds : angle 6.25756 ( 546) Misc. bond : bond 0.00251 ( 5) link_ALPHA1-3 : bond 0.01025 ( 3) link_ALPHA1-3 : angle 1.44087 ( 9) link_ALPHA1-6 : bond 0.00763 ( 3) link_ALPHA1-6 : angle 2.18835 ( 9) link_BETA1-4 : bond 0.00485 ( 12) link_BETA1-4 : angle 2.05602 ( 36) link_NAG-ASN : bond 0.00393 ( 9) link_NAG-ASN : angle 2.34844 ( 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 93 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2938 ASP cc_start: 0.0496 (OUTLIER) cc_final: 0.0170 (p0) REVERT: B 3462 TYR cc_start: 0.9113 (m-10) cc_final: 0.8748 (m-10) outliers start: 33 outliers final: 24 residues processed: 89 average time/residue: 0.0779 time to fit residues: 11.2016 Evaluate side-chains 80 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2938 ASP 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 3168 LYS Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3235 ASP 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 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3707 CYS Chi-restraints excluded: chain B residue 3774 ILE 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: 6.9990 chunk 100 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 0.3980 chunk 140 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4166 GLN B3088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.175956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144015 restraints weight = 23414.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143452 restraints weight = 40281.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141579 restraints weight = 35752.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140192 restraints weight = 33519.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138845 restraints weight = 32155.238| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12178 Z= 0.125 Angle : 0.636 10.358 16593 Z= 0.313 Chirality : 0.047 0.250 1777 Planarity : 0.004 0.055 2163 Dihedral : 7.015 56.892 2222 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.41 % Allowed : 19.98 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.22), residues: 1432 helix: -1.72 (0.96), residues: 32 sheet: -0.25 (0.33), residues: 257 loop : -0.82 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B3150 TYR 0.013 0.001 TYR A4287 PHE 0.014 0.001 PHE B3297 TRP 0.010 0.001 TRP B3288 HIS 0.008 0.001 HIS B3088 Details of bonding type rmsd covalent geometry : bond 0.00287 (12082) covalent geometry : angle 0.61912 (16384) SS BOND : bond 0.00198 ( 64) SS BOND : angle 0.89181 ( 128) hydrogen bonds : bond 0.02936 ( 251) hydrogen bonds : angle 6.18059 ( 546) Misc. bond : bond 0.00202 ( 5) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 1.41980 ( 9) link_ALPHA1-6 : bond 0.00702 ( 3) link_ALPHA1-6 : angle 2.15179 ( 9) link_BETA1-4 : bond 0.00485 ( 12) link_BETA1-4 : angle 1.97155 ( 36) link_NAG-ASN : bond 0.00361 ( 9) link_NAG-ASN : angle 2.27700 ( 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 88 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2914 GLN cc_start: 0.4369 (OUTLIER) cc_final: 0.3931 (pp30) REVERT: B 2938 ASP cc_start: 0.0635 (OUTLIER) cc_final: 0.0402 (p0) REVERT: B 3341 ASP cc_start: 0.8290 (t0) cc_final: 0.7908 (t0) REVERT: B 3413 PHE cc_start: 0.8459 (t80) cc_final: 0.8248 (t80) REVERT: B 3797 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6381 (mpt) outliers start: 31 outliers final: 25 residues processed: 83 average time/residue: 0.0867 time to fit residues: 11.1908 Evaluate side-chains 84 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4166 GLN 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 2914 GLN Chi-restraints excluded: chain B residue 2938 ASP 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 3168 LYS 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 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 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3707 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4166 GLN B3126 HIS B3722 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.175118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145688 restraints weight = 23321.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140510 restraints weight = 38176.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137914 restraints weight = 40661.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137621 restraints weight = 40700.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136107 restraints weight = 31543.509| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12178 Z= 0.168 Angle : 0.663 10.262 16593 Z= 0.327 Chirality : 0.048 0.236 1777 Planarity : 0.004 0.056 2163 Dihedral : 7.030 56.546 2222 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.72 % Allowed : 19.91 % 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 aren not related in a simple way. whole: -1.12 (0.22), residues: 1432 helix: -1.78 (0.97), residues: 32 sheet: -0.27 (0.33), residues: 257 loop : -0.88 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4167 TYR 0.013 0.002 TYR B3136 PHE 0.016 0.001 PHE B3393 TRP 0.013 0.001 TRP A4180 HIS 0.005 0.001 HIS B3732 Details of bonding type rmsd covalent geometry : bond 0.00392 (12082) covalent geometry : angle 0.64530 (16384) SS BOND : bond 0.00236 ( 64) SS BOND : angle 1.02192 ( 128) hydrogen bonds : bond 0.03054 ( 251) hydrogen bonds : angle 6.20582 ( 546) Misc. bond : bond 0.00193 ( 5) link_ALPHA1-3 : bond 0.00936 ( 3) link_ALPHA1-3 : angle 1.44430 ( 9) link_ALPHA1-6 : bond 0.00712 ( 3) link_ALPHA1-6 : angle 2.20050 ( 9) link_BETA1-4 : bond 0.00478 ( 12) link_BETA1-4 : angle 1.96418 ( 36) link_NAG-ASN : bond 0.00356 ( 9) link_NAG-ASN : angle 2.26317 ( 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 89 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2914 GLN cc_start: 0.4408 (OUTLIER) cc_final: 0.3951 (pp30) REVERT: B 2938 ASP cc_start: 0.0783 (OUTLIER) cc_final: 0.0525 (p0) REVERT: B 3797 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6425 (mpt) outliers start: 35 outliers final: 27 residues processed: 84 average time/residue: 0.0834 time to fit residues: 11.0308 Evaluate side-chains 85 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4166 GLN 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 2914 GLN Chi-restraints excluded: chain B residue 2938 ASP 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 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3348 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 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3707 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET 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: 0.0470 chunk 142 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 chunk 59 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.176484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145978 restraints weight = 23604.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143260 restraints weight = 40531.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140627 restraints weight = 38517.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.139734 restraints weight = 35751.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137160 restraints weight = 34201.854| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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 : 0.002 0.053 12178 Z= 0.111 Angle : 0.626 9.725 16593 Z= 0.310 Chirality : 0.046 0.253 1777 Planarity : 0.004 0.056 2163 Dihedral : 6.695 57.480 2222 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.94 % Allowed : 20.68 % 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 aren not related in a simple way. whole: -1.05 (0.22), residues: 1432 helix: -1.69 (0.97), residues: 32 sheet: -0.21 (0.32), residues: 267 loop : -0.84 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4167 TYR 0.013 0.001 TYR A4287 PHE 0.011 0.001 PHE B3205 TRP 0.011 0.001 TRP B3288 HIS 0.004 0.001 HIS B3732 Details of bonding type rmsd covalent geometry : bond 0.00249 (12082) covalent geometry : angle 0.61113 (16384) SS BOND : bond 0.00222 ( 64) SS BOND : angle 0.76394 ( 128) hydrogen bonds : bond 0.02847 ( 251) hydrogen bonds : angle 6.08484 ( 546) Misc. bond : bond 0.00180 ( 5) link_ALPHA1-3 : bond 0.00969 ( 3) link_ALPHA1-3 : angle 1.39058 ( 9) link_ALPHA1-6 : bond 0.00672 ( 3) link_ALPHA1-6 : angle 2.02242 ( 9) link_BETA1-4 : bond 0.00494 ( 12) link_BETA1-4 : angle 1.82738 ( 36) link_NAG-ASN : bond 0.00371 ( 9) link_NAG-ASN : angle 2.25794 ( 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 84 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2914 GLN cc_start: 0.4363 (OUTLIER) cc_final: 0.3914 (pp30) REVERT: B 2938 ASP cc_start: 0.0780 (OUTLIER) cc_final: 0.0540 (p0) REVERT: B 3341 ASP cc_start: 0.8186 (t0) cc_final: 0.7848 (t0) REVERT: B 3462 TYR cc_start: 0.9071 (m-10) cc_final: 0.8709 (m-10) REVERT: B 3797 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6402 (mpt) outliers start: 25 outliers final: 21 residues processed: 79 average time/residue: 0.0827 time to fit residues: 10.6202 Evaluate side-chains 80 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4166 GLN 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 2914 GLN Chi-restraints excluded: chain B residue 2938 ASP Chi-restraints excluded: chain B residue 3002 CYS Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3079 LEU 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 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3707 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET 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: 0.6980 chunk 127 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.175834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144262 restraints weight = 23439.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143815 restraints weight = 41403.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142129 restraints weight = 35966.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141360 restraints weight = 35863.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140278 restraints weight = 34681.389| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12178 Z= 0.136 Angle : 0.631 9.886 16593 Z= 0.312 Chirality : 0.046 0.239 1777 Planarity : 0.004 0.057 2163 Dihedral : 6.642 57.559 2222 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.26 % Allowed : 20.53 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.22), residues: 1432 helix: -1.67 (0.98), residues: 32 sheet: -0.18 (0.32), residues: 265 loop : -0.85 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4167 TYR 0.013 0.001 TYR A4287 PHE 0.043 0.001 PHE B3413 TRP 0.011 0.001 TRP B3427 HIS 0.004 0.001 HIS B3732 Details of bonding type rmsd covalent geometry : bond 0.00317 (12082) covalent geometry : angle 0.61523 (16384) SS BOND : bond 0.00206 ( 64) SS BOND : angle 0.85369 ( 128) hydrogen bonds : bond 0.02899 ( 251) hydrogen bonds : angle 6.07376 ( 546) Misc. bond : bond 0.00185 ( 5) link_ALPHA1-3 : bond 0.00923 ( 3) link_ALPHA1-3 : angle 1.39945 ( 9) link_ALPHA1-6 : bond 0.00649 ( 3) link_ALPHA1-6 : angle 2.02494 ( 9) link_BETA1-4 : bond 0.00487 ( 12) link_BETA1-4 : angle 1.82865 ( 36) link_NAG-ASN : bond 0.00348 ( 9) link_NAG-ASN : angle 2.23733 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1711.65 seconds wall clock time: 30 minutes 22.22 seconds (1822.22 seconds total)