Starting phenix.real_space_refine on Wed May 14 17:51:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx9_36693/05_2025/8jx9_36693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx9_36693/05_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_36693/05_2025/8jx9_36693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx9_36693/05_2025/8jx9_36693.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx9_36693/05_2025/8jx9_36693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx9_36693/05_2025/8jx9_36693.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 20 9.91 5 S 149 5.16 5 C 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.91, per 1000 atoms: 0.58 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: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 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: 1.68 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: 4.74 Time building geometry restraints manager: 3.61 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: 0.840 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (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 TRP 0.011 0.001 TRP B3531 HIS 0.004 0.001 HIS B3732 PHE 0.016 0.001 PHE B3000 TYR 0.013 0.001 TYR B3202 ARG 0.007 0.000 ARG B3635 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 9) link_NAG-ASN : angle 4.24648 ( 27) 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_ALPHA1-3 : bond 0.00234 ( 3) link_ALPHA1-3 : angle 1.05516 ( 9) hydrogen bonds : bond 0.24352 ( 251) hydrogen bonds : angle 10.13296 ( 546) SS BOND : bond 0.00234 ( 64) SS BOND : angle 0.83442 ( 128) covalent geometry : bond 0.00425 (12082) covalent geometry : angle 0.80220 (16384) Misc. bond : bond 0.34167 ( 5) *********************** 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 : 1.207 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: 0.7600 (mp) REVERT: A 4165 SER cc_start: 0.6779 (m) cc_final: 0.5969 (p) REVERT: A 4187 ASP cc_start: 0.8184 (t0) cc_final: 0.7929 (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: 0.8013 (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: 0.8296 (p0) REVERT: B 3897 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6363 (ppp80) outliers start: 29 outliers final: 15 residues processed: 99 average time/residue: 0.2638 time to fit residues: 38.0584 Evaluate side-chains 82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 120 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 112 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3057 ASN B3066 GLN ** B3207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3602 GLN B3733 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.177591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153530 restraints weight = 23263.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.148644 restraints weight = 32622.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.145330 restraints weight = 37533.746| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12178 Z= 0.127 Angle : 0.677 9.777 16593 Z= 0.334 Chirality : 0.048 0.279 1777 Planarity : 0.004 0.055 2163 Dihedral : 11.972 89.133 2243 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.57 % Allowed : 16.64 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1432 helix: -2.15 (1.15), residues: 20 sheet: -0.27 (0.32), residues: 260 loop : -0.68 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4160 HIS 0.006 0.001 HIS A4387 PHE 0.011 0.001 PHE B3135 TYR 0.014 0.002 TYR A4287 ARG 0.003 0.000 ARG A4176 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 9) link_NAG-ASN : angle 3.08957 ( 27) link_ALPHA1-6 : bond 0.00644 ( 3) link_ALPHA1-6 : angle 1.90515 ( 9) link_BETA1-4 : bond 0.00677 ( 12) link_BETA1-4 : angle 2.77002 ( 36) link_ALPHA1-3 : bond 0.00713 ( 3) link_ALPHA1-3 : angle 2.33220 ( 9) hydrogen bonds : bond 0.04239 ( 251) hydrogen bonds : angle 7.30245 ( 546) SS BOND : bond 0.00239 ( 64) SS BOND : angle 0.69640 ( 128) covalent geometry : bond 0.00275 (12082) covalent geometry : angle 0.65020 (16384) Misc. bond : bond 0.00626 ( 5) *********************** 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 101 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4090 ASP cc_start: 0.0635 (OUTLIER) cc_final: 0.0058 (m-30) REVERT: B 3258 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9023 (tp) REVERT: B 3683 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7204 (m-70) REVERT: B 3897 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6690 (ppp80) outliers start: 33 outliers final: 12 residues processed: 97 average time/residue: 0.2441 time to fit residues: 35.0758 Evaluate side-chains 72 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 4246 VAL Chi-restraints excluded: chain A residue 4359 SER Chi-restraints excluded: chain A residue 4412 CYS Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3258 LEU 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 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 33 optimal weight: 50.0000 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 50.0000 chunk 8 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 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 = 0.176083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.148598 restraints weight = 23455.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147535 restraints weight = 42059.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145328 restraints weight = 37449.023| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12178 Z= 0.175 Angle : 0.678 10.056 16593 Z= 0.336 Chirality : 0.048 0.191 1777 Planarity : 0.004 0.045 2163 Dihedral : 10.863 86.672 2231 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.34 % Allowed : 16.17 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1432 helix: -1.78 (1.07), residues: 26 sheet: -0.36 (0.32), residues: 269 loop : -0.75 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4160 HIS 0.006 0.001 HIS B3331 PHE 0.018 0.001 PHE B3393 TYR 0.014 0.002 TYR B3244 ARG 0.003 0.000 ARG B2961 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 9) link_NAG-ASN : angle 2.61309 ( 27) link_ALPHA1-6 : bond 0.00747 ( 3) link_ALPHA1-6 : angle 1.94747 ( 9) link_BETA1-4 : bond 0.00495 ( 12) link_BETA1-4 : angle 2.62915 ( 36) link_ALPHA1-3 : bond 0.00893 ( 3) link_ALPHA1-3 : angle 1.46192 ( 9) hydrogen bonds : bond 0.03853 ( 251) hydrogen bonds : angle 6.92609 ( 546) SS BOND : bond 0.00294 ( 64) SS BOND : angle 0.77223 ( 128) covalent geometry : bond 0.00401 (12082) covalent geometry : angle 0.65629 (16384) Misc. bond : bond 0.00170 ( 5) *********************** 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 103 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 60 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4083 GLU cc_start: 0.3686 (OUTLIER) cc_final: -0.0513 (tp30) REVERT: B 2938 ASP cc_start: 0.0465 (OUTLIER) cc_final: 0.0229 (p0) REVERT: B 3452 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8744 (mttt) REVERT: B 3683 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.7190 (m-70) REVERT: B 3797 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6908 (mpt) REVERT: B 3897 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6714 (ppp80) outliers start: 43 outliers final: 22 residues processed: 98 average time/residue: 0.2442 time to fit residues: 36.2682 Evaluate side-chains 85 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4083 GLU Chi-restraints excluded: chain A residue 4100 LEU Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER Chi-restraints excluded: chain A residue 4172 THR Chi-restraints excluded: chain A residue 4246 VAL Chi-restraints excluded: chain A residue 4412 CYS Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 2938 ASP Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3040 THR Chi-restraints excluded: chain B residue 3148 ASP Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3271 LEU 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 3452 LYS 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 3797 MET Chi-restraints excluded: chain B residue 3870 VAL Chi-restraints excluded: chain B residue 3883 ILE Chi-restraints excluded: chain B residue 3897 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 131 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 69 optimal weight: 0.0270 chunk 120 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 96 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.178027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.148423 restraints weight = 23270.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146394 restraints weight = 36767.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144792 restraints weight = 34910.779| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12178 Z= 0.107 Angle : 0.615 9.524 16593 Z= 0.304 Chirality : 0.046 0.204 1777 Planarity : 0.004 0.044 2163 Dihedral : 9.220 73.573 2230 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.95 % Allowed : 17.26 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1432 helix: -1.61 (1.07), residues: 26 sheet: -0.29 (0.32), residues: 269 loop : -0.68 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4160 HIS 0.003 0.000 HIS B3732 PHE 0.011 0.001 PHE B3205 TYR 0.014 0.001 TYR A4287 ARG 0.003 0.000 ARG A4156 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 9) link_NAG-ASN : angle 2.25669 ( 27) link_ALPHA1-6 : bond 0.00727 ( 3) link_ALPHA1-6 : angle 1.97408 ( 9) link_BETA1-4 : bond 0.00514 ( 12) link_BETA1-4 : angle 2.37763 ( 36) link_ALPHA1-3 : bond 0.01015 ( 3) link_ALPHA1-3 : angle 1.60001 ( 9) hydrogen bonds : bond 0.03085 ( 251) hydrogen bonds : angle 6.50092 ( 546) SS BOND : bond 0.00203 ( 64) SS BOND : angle 0.66940 ( 128) covalent geometry : bond 0.00233 (12082) covalent geometry : angle 0.59638 (16384) Misc. bond : bond 0.00173 ( 5) *********************** 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 101 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4083 GLU cc_start: 0.3434 (OUTLIER) cc_final: -0.0372 (tp30) REVERT: B 2938 ASP cc_start: 0.0465 (OUTLIER) cc_final: 0.0189 (p0) REVERT: B 3452 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8466 (mttt) REVERT: B 3462 TYR cc_start: 0.9055 (m-10) cc_final: 0.8717 (m-10) REVERT: B 3683 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.7304 (m-70) REVERT: B 3797 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6741 (mpt) REVERT: B 3897 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6655 (ppp80) outliers start: 38 outliers final: 15 residues processed: 96 average time/residue: 0.2441 time to fit residues: 34.7263 Evaluate side-chains 76 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4083 GLU Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER Chi-restraints excluded: chain A residue 4412 CYS Chi-restraints excluded: chain B residue 1225 THR 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 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS 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 Chi-restraints excluded: chain B residue 3897 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 59 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4145 GLN B3207 ASN B3722 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.176654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.149860 restraints weight = 23281.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.146986 restraints weight = 42359.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145446 restraints weight = 44012.895| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12178 Z= 0.146 Angle : 0.638 10.027 16593 Z= 0.315 Chirality : 0.047 0.190 1777 Planarity : 0.004 0.050 2163 Dihedral : 8.181 53.961 2230 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.80 % Allowed : 17.73 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1432 helix: -1.35 (1.10), residues: 26 sheet: -0.46 (0.32), residues: 273 loop : -0.73 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A4160 HIS 0.004 0.001 HIS B3331 PHE 0.015 0.001 PHE B3393 TYR 0.014 0.002 TYR A4287 ARG 0.003 0.000 ARG B2961 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 2.22321 ( 27) link_ALPHA1-6 : bond 0.00706 ( 3) link_ALPHA1-6 : angle 2.17270 ( 9) link_BETA1-4 : bond 0.00516 ( 12) link_BETA1-4 : angle 2.30991 ( 36) link_ALPHA1-3 : bond 0.00960 ( 3) link_ALPHA1-3 : angle 1.59278 ( 9) hydrogen bonds : bond 0.03145 ( 251) hydrogen bonds : angle 6.40113 ( 546) SS BOND : bond 0.00228 ( 64) SS BOND : angle 0.70854 ( 128) covalent geometry : bond 0.00338 (12082) covalent geometry : angle 0.62041 (16384) Misc. bond : bond 0.00238 ( 5) *********************** 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 93 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 57 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2938 ASP cc_start: 0.0479 (OUTLIER) cc_final: 0.0244 (p0) REVERT: B 3452 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8474 (mttt) REVERT: B 3683 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7327 (m-70) REVERT: B 3797 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6737 (mpt) outliers start: 36 outliers final: 23 residues processed: 89 average time/residue: 0.2387 time to fit residues: 32.1275 Evaluate side-chains 81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER Chi-restraints excluded: chain A residue 4246 VAL Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 2938 ASP Chi-restraints excluded: chain B residue 3008 VAL Chi-restraints excluded: chain B residue 3079 LEU Chi-restraints excluded: chain B residue 3172 VAL Chi-restraints excluded: chain B residue 3207 ASN Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 15 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 17 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 0.0040 chunk 33 optimal weight: 50.0000 chunk 53 optimal weight: 0.4980 chunk 16 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4166 GLN B3207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.176896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146483 restraints weight = 23428.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143187 restraints weight = 37782.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140639 restraints weight = 42065.663| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.1855 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= 0.126 Angle : 0.619 9.877 16593 Z= 0.306 Chirality : 0.046 0.192 1777 Planarity : 0.004 0.053 2163 Dihedral : 7.579 54.319 2225 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.03 % Allowed : 17.96 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1432 helix: -1.22 (1.11), residues: 26 sheet: -0.44 (0.32), residues: 272 loop : -0.72 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A4160 HIS 0.008 0.001 HIS B3088 PHE 0.018 0.001 PHE B3135 TYR 0.013 0.001 TYR A4287 ARG 0.003 0.000 ARG B3017 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 9) link_NAG-ASN : angle 2.12442 ( 27) link_ALPHA1-6 : bond 0.00740 ( 3) link_ALPHA1-6 : angle 2.21268 ( 9) link_BETA1-4 : bond 0.00487 ( 12) link_BETA1-4 : angle 2.11447 ( 36) link_ALPHA1-3 : bond 0.01013 ( 3) link_ALPHA1-3 : angle 1.48982 ( 9) hydrogen bonds : bond 0.02963 ( 251) hydrogen bonds : angle 6.29676 ( 546) SS BOND : bond 0.00221 ( 64) SS BOND : angle 0.68469 ( 128) covalent geometry : bond 0.00286 (12082) covalent geometry : angle 0.60314 (16384) Misc. bond : bond 0.00167 ( 5) *********************** 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 97 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 58 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3341 ASP cc_start: 0.8476 (t0) cc_final: 0.8136 (t0) REVERT: B 3452 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8508 (mttt) REVERT: B 3683 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7338 (m-70) REVERT: B 3797 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6704 (mpt) outliers start: 39 outliers final: 27 residues processed: 90 average time/residue: 0.2170 time to fit residues: 30.2853 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 : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER 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 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 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3507 ARG Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 42 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 114 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.176396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145406 restraints weight = 23453.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141331 restraints weight = 40722.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.137737 restraints weight = 41997.841| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12178 Z= 0.143 Angle : 0.624 9.960 16593 Z= 0.307 Chirality : 0.047 0.193 1777 Planarity : 0.004 0.054 2163 Dihedral : 7.305 54.257 2225 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.03 % Allowed : 17.81 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1432 helix: -1.09 (1.13), residues: 26 sheet: -0.45 (0.32), residues: 273 loop : -0.72 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A4160 HIS 0.003 0.001 HIS B3732 PHE 0.014 0.001 PHE B3135 TYR 0.013 0.001 TYR A4287 ARG 0.006 0.000 ARG B3897 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 9) link_NAG-ASN : angle 2.07376 ( 27) link_ALPHA1-6 : bond 0.00735 ( 3) link_ALPHA1-6 : angle 2.23841 ( 9) link_BETA1-4 : bond 0.00495 ( 12) link_BETA1-4 : angle 2.03374 ( 36) link_ALPHA1-3 : bond 0.00974 ( 3) link_ALPHA1-3 : angle 1.44205 ( 9) hydrogen bonds : bond 0.03004 ( 251) hydrogen bonds : angle 6.24948 ( 546) SS BOND : bond 0.00216 ( 64) SS BOND : angle 0.71106 ( 128) covalent geometry : bond 0.00329 (12082) covalent geometry : angle 0.60843 (16384) Misc. bond : bond 0.00153 ( 5) *********************** 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 96 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 57 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4160 TRP cc_start: 0.7288 (p90) cc_final: 0.6984 (p90) REVERT: A 4169 GLU cc_start: 0.5887 (mm-30) cc_final: 0.5574 (mm-30) REVERT: B 2938 ASP cc_start: 0.0703 (OUTLIER) cc_final: 0.0457 (p0) REVERT: B 3341 ASP cc_start: 0.8262 (t0) cc_final: 0.7906 (t0) REVERT: B 3452 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8507 (mttt) REVERT: B 3683 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7304 (m-70) REVERT: B 3797 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6631 (mpt) outliers start: 39 outliers final: 28 residues processed: 92 average time/residue: 0.2030 time to fit residues: 29.4777 Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER Chi-restraints excluded: chain A residue 4279 LEU Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 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 3172 VAL Chi-restraints excluded: chain B residue 3207 ASN Chi-restraints excluded: chain B residue 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3534 CYS Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3707 CYS Chi-restraints excluded: chain B residue 3744 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 21 optimal weight: 50.0000 chunk 80 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4166 GLN B3207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.176977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148203 restraints weight = 23467.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144012 restraints weight = 37856.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141535 restraints weight = 36783.596| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2024 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= 0.122 Angle : 0.615 9.860 16593 Z= 0.304 Chirality : 0.046 0.195 1777 Planarity : 0.004 0.055 2163 Dihedral : 7.025 54.561 2225 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.80 % Allowed : 18.20 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1432 helix: -1.05 (1.13), residues: 26 sheet: -0.41 (0.32), residues: 273 loop : -0.70 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A4160 HIS 0.003 0.001 HIS B3732 PHE 0.013 0.001 PHE B3135 TYR 0.013 0.001 TYR A4287 ARG 0.005 0.000 ARG B3897 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 9) link_NAG-ASN : angle 2.07221 ( 27) link_ALPHA1-6 : bond 0.00709 ( 3) link_ALPHA1-6 : angle 2.13681 ( 9) link_BETA1-4 : bond 0.00488 ( 12) link_BETA1-4 : angle 1.92097 ( 36) link_ALPHA1-3 : bond 0.01012 ( 3) link_ALPHA1-3 : angle 1.42261 ( 9) hydrogen bonds : bond 0.02894 ( 251) hydrogen bonds : angle 6.14995 ( 546) SS BOND : bond 0.00192 ( 64) SS BOND : angle 0.66519 ( 128) covalent geometry : bond 0.00278 (12082) covalent geometry : angle 0.60034 (16384) Misc. bond : bond 0.00315 ( 5) *********************** 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 96 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2938 ASP cc_start: 0.0251 (OUTLIER) cc_final: -0.0029 (p0) REVERT: B 3341 ASP cc_start: 0.8364 (t0) cc_final: 0.8027 (t0) REVERT: B 3452 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8456 (mttt) REVERT: B 3462 TYR cc_start: 0.9117 (m-10) cc_final: 0.8742 (m-10) REVERT: B 3683 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7370 (m-70) REVERT: B 3797 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6313 (mpt) outliers start: 36 outliers final: 25 residues processed: 91 average time/residue: 0.2028 time to fit residues: 28.9436 Evaluate side-chains 84 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 55 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER 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 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 3235 ASP Chi-restraints excluded: chain B residue 3292 ILE Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3431 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 3592 GLU Chi-restraints excluded: chain B residue 3644 CYS Chi-restraints excluded: chain B residue 3683 HIS Chi-restraints excluded: chain B residue 3707 CYS Chi-restraints excluded: chain B residue 3744 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 3 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 80 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 132 optimal weight: 0.0870 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4166 GLN B3789 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.177545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146001 restraints weight = 23335.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143913 restraints weight = 40168.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141205 restraints weight = 38505.545| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12178 Z= 0.111 Angle : 0.619 13.679 16593 Z= 0.305 Chirality : 0.046 0.201 1777 Planarity : 0.004 0.056 2163 Dihedral : 6.714 54.916 2224 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.49 % Allowed : 19.13 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1432 helix: -1.02 (1.14), residues: 26 sheet: -0.37 (0.31), residues: 283 loop : -0.70 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B3288 HIS 0.003 0.001 HIS B3732 PHE 0.038 0.001 PHE B3413 TYR 0.013 0.001 TYR A4287 ARG 0.011 0.000 ARG A4167 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 9) link_NAG-ASN : angle 2.04945 ( 27) link_ALPHA1-6 : bond 0.00667 ( 3) link_ALPHA1-6 : angle 2.03496 ( 9) link_BETA1-4 : bond 0.00498 ( 12) link_BETA1-4 : angle 1.83126 ( 36) link_ALPHA1-3 : bond 0.00985 ( 3) link_ALPHA1-3 : angle 1.37081 ( 9) hydrogen bonds : bond 0.02801 ( 251) hydrogen bonds : angle 6.04281 ( 546) SS BOND : bond 0.00180 ( 64) SS BOND : angle 0.65054 ( 128) covalent geometry : bond 0.00249 (12082) covalent geometry : angle 0.60596 (16384) Misc. bond : bond 0.00226 ( 5) *********************** 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: 32 poor density : 57 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2936 MET cc_start: 0.3306 (tmm) cc_final: 0.1965 (mtm) REVERT: B 2938 ASP cc_start: 0.0681 (OUTLIER) cc_final: 0.0316 (p0) REVERT: B 3341 ASP cc_start: 0.8207 (t0) cc_final: 0.7899 (t0) REVERT: B 3452 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8498 (mttt) REVERT: B 3462 TYR cc_start: 0.9095 (m-10) cc_final: 0.8731 (m-10) REVERT: B 3797 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6200 (mpt) outliers start: 32 outliers final: 24 residues processed: 83 average time/residue: 0.2060 time to fit residues: 26.7776 Evaluate side-chains 82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER Chi-restraints excluded: chain A residue 4166 GLN Chi-restraints excluded: chain A residue 4172 THR Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 2933 CYS 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 3235 ASP Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 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 132 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 0.0060 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.177397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145603 restraints weight = 23275.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142444 restraints weight = 38693.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140927 restraints weight = 42113.196| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12178 Z= 0.123 Angle : 0.622 13.432 16593 Z= 0.306 Chirality : 0.046 0.260 1777 Planarity : 0.004 0.056 2163 Dihedral : 6.514 54.909 2222 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.10 % Allowed : 19.44 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1432 helix: -0.98 (1.14), residues: 26 sheet: -0.28 (0.31), residues: 281 loop : -0.71 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B3288 HIS 0.003 0.001 HIS B3732 PHE 0.035 0.001 PHE B3413 TYR 0.013 0.001 TYR A4287 ARG 0.008 0.000 ARG A4167 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 9) link_NAG-ASN : angle 2.26060 ( 27) link_ALPHA1-6 : bond 0.00627 ( 3) link_ALPHA1-6 : angle 1.99503 ( 9) link_BETA1-4 : bond 0.00490 ( 12) link_BETA1-4 : angle 1.80256 ( 36) link_ALPHA1-3 : bond 0.00944 ( 3) link_ALPHA1-3 : angle 1.37958 ( 9) hydrogen bonds : bond 0.02856 ( 251) hydrogen bonds : angle 5.98013 ( 546) SS BOND : bond 0.00184 ( 64) SS BOND : angle 0.66272 ( 128) covalent geometry : bond 0.00282 (12082) covalent geometry : angle 0.60755 (16384) Misc. bond : bond 0.00222 ( 5) ********************** 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 82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2936 MET cc_start: 0.3384 (tmm) cc_final: 0.2024 (mtm) REVERT: B 2938 ASP cc_start: 0.0424 (OUTLIER) cc_final: 0.0100 (p0) REVERT: B 3341 ASP cc_start: 0.8053 (t0) cc_final: 0.7776 (t0) REVERT: B 3452 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8482 (mttt) REVERT: B 3462 TYR cc_start: 0.9100 (m-10) cc_final: 0.8725 (m-10) REVERT: B 3797 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6251 (mpt) outliers start: 27 outliers final: 22 residues processed: 77 average time/residue: 0.2081 time to fit residues: 25.5144 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 : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4141 LYS Chi-restraints excluded: chain A residue 4144 MET Chi-restraints excluded: chain A residue 4165 SER Chi-restraints excluded: chain A residue 4166 GLN Chi-restraints excluded: chain A residue 4172 THR Chi-restraints excluded: chain B residue 1225 THR Chi-restraints excluded: chain B residue 1261 SER Chi-restraints excluded: chain B residue 1271 THR Chi-restraints excluded: chain B residue 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 3235 ASP Chi-restraints excluded: chain B residue 3416 THR Chi-restraints excluded: chain B residue 3429 THR Chi-restraints excluded: chain B residue 3452 LYS Chi-restraints excluded: chain B residue 3478 CYS Chi-restraints excluded: chain B residue 3511 MET Chi-restraints excluded: chain B residue 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 139 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 40.0000 chunk 68 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 104 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.177565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146494 restraints weight = 23132.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142088 restraints weight = 39008.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.137740 restraints weight = 44058.064| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12178 Z= 0.115 Angle : 0.614 13.383 16593 Z= 0.303 Chirality : 0.046 0.254 1777 Planarity : 0.004 0.056 2163 Dihedral : 6.380 55.056 2222 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.18 % Allowed : 19.44 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1432 helix: -1.29 (1.14), residues: 26 sheet: -0.31 (0.31), residues: 286 loop : -0.68 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A4160 HIS 0.003 0.001 HIS B3732 PHE 0.032 0.001 PHE B3413 TYR 0.013 0.001 TYR A4287 ARG 0.008 0.000 ARG A4167 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 9) link_NAG-ASN : angle 2.19350 ( 27) link_ALPHA1-6 : bond 0.00613 ( 3) link_ALPHA1-6 : angle 1.93729 ( 9) link_BETA1-4 : bond 0.00499 ( 12) link_BETA1-4 : angle 1.76291 ( 36) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 1.37357 ( 9) hydrogen bonds : bond 0.02844 ( 251) hydrogen bonds : angle 5.99245 ( 546) SS BOND : bond 0.00181 ( 64) SS BOND : angle 0.65690 ( 128) covalent geometry : bond 0.00260 (12082) covalent geometry : angle 0.60029 (16384) Misc. bond : bond 0.00201 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.72 seconds wall clock time: 57 minutes 47.64 seconds (3467.64 seconds total)