Starting phenix.real_space_refine on Wed Sep 17 22:27:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jwg_61852/09_2025/9jwg_61852_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jwg_61852/09_2025/9jwg_61852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jwg_61852/09_2025/9jwg_61852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jwg_61852/09_2025/9jwg_61852.map" model { file = "/net/cci-nas-00/data/ceres_data/9jwg_61852/09_2025/9jwg_61852_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jwg_61852/09_2025/9jwg_61852_neut.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 7421 2.51 5 N 2024 2.21 5 O 2138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11647 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1872 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 211} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 9775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9775 Classifications: {'peptide': 1221} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 62, 'TRANS': 1158} Chain breaks: 6 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.97, per 1000 atoms: 0.26 Number of scatterers: 11647 At special positions: 0 Unit cell: (133.985, 124.49, 112.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2138 8.00 N 2024 7.00 C 7421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 612.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2802 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 3 sheets defined 56.2% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 38 through 51 Processing helix chain 'B' and resid 57 through 72 Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.846A pdb=" N LEU B 233 " --> pdb=" O VAL B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'A' and resid 3711 through 3730 removed outlier: 4.097A pdb=" N VAL A3724 " --> pdb=" O GLU A3720 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A3728 " --> pdb=" O VAL A3724 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A3730 " --> pdb=" O ALA A3726 " (cutoff:3.500A) Processing helix chain 'A' and resid 3731 through 3733 No H-bonds generated for 'chain 'A' and resid 3731 through 3733' Processing helix chain 'A' and resid 3734 through 3746 removed outlier: 4.249A pdb=" N VAL A3740 " --> pdb=" O PRO A3736 " (cutoff:3.500A) Processing helix chain 'A' and resid 3746 through 3754 Processing helix chain 'A' and resid 3758 through 3774 removed outlier: 4.166A pdb=" N LYS A3769 " --> pdb=" O GLN A3765 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A3772 " --> pdb=" O LEU A3768 " (cutoff:3.500A) Processing helix chain 'A' and resid 3780 through 3801 removed outlier: 4.082A pdb=" N ALA A3801 " --> pdb=" O LYS A3797 " (cutoff:3.500A) Processing helix chain 'A' and resid 3810 through 3821 removed outlier: 4.186A pdb=" N VAL A3814 " --> pdb=" O SER A3810 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A3815 " --> pdb=" O LEU A3811 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3835 removed outlier: 3.908A pdb=" N LEU A3825 " --> pdb=" O PHE A3821 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A3835 " --> pdb=" O ILE A3831 " (cutoff:3.500A) Processing helix chain 'A' and resid 3836 through 3844 removed outlier: 3.659A pdb=" N HIS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A3844 " --> pdb=" O HIS A3840 " (cutoff:3.500A) Processing helix chain 'A' and resid 3857 through 3873 Processing helix chain 'A' and resid 3879 through 3898 removed outlier: 4.519A pdb=" N MET A3891 " --> pdb=" O LYS A3887 " (cutoff:3.500A) Proline residue: A3892 - end of helix Processing helix chain 'A' and resid 3899 through 3902 removed outlier: 3.615A pdb=" N MET A3902 " --> pdb=" O ASP A3899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3899 through 3902' Processing helix chain 'A' and resid 3906 through 3926 removed outlier: 3.873A pdb=" N ARG A3922 " --> pdb=" O ALA A3918 " (cutoff:3.500A) Processing helix chain 'A' and resid 3926 through 3933 Processing helix chain 'A' and resid 3936 through 3941 removed outlier: 3.716A pdb=" N ARG A3940 " --> pdb=" O GLY A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3943 through 3961 removed outlier: 4.181A pdb=" N LEU A3947 " --> pdb=" O GLU A3943 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A3951 " --> pdb=" O LEU A3947 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A3953 " --> pdb=" O THR A3949 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A3954 " --> pdb=" O GLU A3950 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3967 through 3990 Processing helix chain 'A' and resid 4021 through 4027 Processing helix chain 'A' and resid 4048 through 4078 removed outlier: 3.511A pdb=" N ALA A4054 " --> pdb=" O ALA A4050 " (cutoff:3.500A) Processing helix chain 'A' and resid 4085 through 4094 Processing helix chain 'A' and resid 4095 through 4097 No H-bonds generated for 'chain 'A' and resid 4095 through 4097' Processing helix chain 'A' and resid 4132 through 4140 removed outlier: 3.834A pdb=" N LEU A4137 " --> pdb=" O VAL A4133 " (cutoff:3.500A) Processing helix chain 'A' and resid 4146 through 4159 removed outlier: 3.628A pdb=" N LYS A4159 " --> pdb=" O THR A4155 " (cutoff:3.500A) Processing helix chain 'A' and resid 4170 through 4186 removed outlier: 3.595A pdb=" N ASN A4176 " --> pdb=" O MET A4172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A4186 " --> pdb=" O ILE A4182 " (cutoff:3.500A) Processing helix chain 'A' and resid 4193 through 4204 removed outlier: 3.967A pdb=" N GLU A4199 " --> pdb=" O LEU A4195 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A4202 " --> pdb=" O LEU A4198 " (cutoff:3.500A) Processing helix chain 'A' and resid 4222 through 4244 Processing helix chain 'A' and resid 4252 through 4271 removed outlier: 4.020A pdb=" N LYS A4256 " --> pdb=" O MET A4252 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A4260 " --> pdb=" O LYS A4256 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A4271 " --> pdb=" O CYS A4267 " (cutoff:3.500A) Processing helix chain 'A' and resid 4274 through 4287 Processing helix chain 'A' and resid 4288 through 4295 removed outlier: 3.606A pdb=" N VAL A4292 " --> pdb=" O GLY A4288 " (cutoff:3.500A) Processing helix chain 'A' and resid 4310 through 4317 Processing helix chain 'A' and resid 4325 through 4329 removed outlier: 4.103A pdb=" N VAL A4329 " --> pdb=" O ARG A4326 " (cutoff:3.500A) Processing helix chain 'A' and resid 4331 through 4348 removed outlier: 3.875A pdb=" N LYS A4335 " --> pdb=" O GLY A4331 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A4339 " --> pdb=" O LYS A4335 " (cutoff:3.500A) Processing helix chain 'A' and resid 4350 through 4360 removed outlier: 3.961A pdb=" N LYS A4354 " --> pdb=" O PRO A4350 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A4355 " --> pdb=" O LEU A4351 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS A4358 " --> pdb=" O LYS A4354 " (cutoff:3.500A) Processing helix chain 'A' and resid 4363 through 4379 Processing helix chain 'A' and resid 4380 through 4383 Processing helix chain 'A' and resid 4387 through 4391 Processing helix chain 'A' and resid 4393 through 4406 removed outlier: 3.541A pdb=" N CYS A4397 " --> pdb=" O THR A4393 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A4399 " --> pdb=" O GLU A4395 " (cutoff:3.500A) Processing helix chain 'A' and resid 4412 through 4424 Processing helix chain 'A' and resid 4441 through 4457 Processing helix chain 'A' and resid 4459 through 4461 No H-bonds generated for 'chain 'A' and resid 4459 through 4461' Processing helix chain 'A' and resid 4462 through 4469 Processing helix chain 'A' and resid 4575 through 4591 removed outlier: 3.764A pdb=" N LEU A4585 " --> pdb=" O LEU A4581 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A4587 " --> pdb=" O ARG A4583 " (cutoff:3.500A) Processing helix chain 'A' and resid 4592 through 4596 removed outlier: 3.570A pdb=" N GLN A4596 " --> pdb=" O GLY A4593 " (cutoff:3.500A) Processing helix chain 'A' and resid 4597 through 4603 removed outlier: 3.858A pdb=" N LEU A4601 " --> pdb=" O SER A4597 " (cutoff:3.500A) Processing helix chain 'A' and resid 4614 through 4632 removed outlier: 3.600A pdb=" N GLN A4618 " --> pdb=" O GLY A4614 " (cutoff:3.500A) Processing helix chain 'A' and resid 4634 through 4651 Processing helix chain 'A' and resid 4670 through 4686 removed outlier: 3.877A pdb=" N ALA A4683 " --> pdb=" O LYS A4679 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A4684 " --> pdb=" O GLU A4680 " (cutoff:3.500A) Processing helix chain 'A' and resid 4687 through 4690 removed outlier: 3.863A pdb=" N GLU A4690 " --> pdb=" O PRO A4687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4687 through 4690' Processing helix chain 'A' and resid 4694 through 4704 Processing helix chain 'A' and resid 4712 through 4718 Processing helix chain 'A' and resid 4733 through 4737 Processing helix chain 'A' and resid 4748 through 4759 removed outlier: 3.540A pdb=" N HIS A4754 " --> pdb=" O GLU A4750 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A4757 " --> pdb=" O GLN A4753 " (cutoff:3.500A) Processing helix chain 'A' and resid 4765 through 4773 Processing helix chain 'A' and resid 4780 through 4782 No H-bonds generated for 'chain 'A' and resid 4780 through 4782' Processing helix chain 'A' and resid 4783 through 4788 Processing helix chain 'A' and resid 4789 through 4798 removed outlier: 4.203A pdb=" N VAL A4795 " --> pdb=" O GLN A4791 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4816 removed outlier: 3.640A pdb=" N HIS A4816 " --> pdb=" O PHE A4812 " (cutoff:3.500A) Processing helix chain 'A' and resid 4819 through 4838 Processing helix chain 'A' and resid 4839 through 4847 removed outlier: 3.652A pdb=" N GLU A4844 " --> pdb=" O ARG A4840 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A4845 " --> pdb=" O ARG A4841 " (cutoff:3.500A) Processing helix chain 'A' and resid 4874 through 4876 No H-bonds generated for 'chain 'A' and resid 4874 through 4876' Processing helix chain 'A' and resid 4877 through 4899 removed outlier: 3.576A pdb=" N THR A4881 " --> pdb=" O GLY A4877 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A4884 " --> pdb=" O ALA A4880 " (cutoff:3.500A) Processing helix chain 'A' and resid 4916 through 4920 removed outlier: 3.880A pdb=" N VAL A4920 " --> pdb=" O GLU A4917 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4936 Processing helix chain 'A' and resid 4952 through 4962 Processing sheet with id=AA1, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.423A pdb=" N LEU B 76 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 239 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4129 through 4130 Processing sheet with id=AA3, first strand: chain 'A' and resid 4910 through 4911 removed outlier: 6.591A pdb=" N VAL A4910 " --> pdb=" O LEU A4971 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 519 hydrogen bonds defined for protein. 1521 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: 1.99 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1954 1.30 - 1.42: 2891 1.42 - 1.55: 6957 1.55 - 1.68: 3 1.68 - 1.81: 89 Bond restraints: 11894 Sorted by residual: bond pdb=" CA LEU A3934 " pdb=" C LEU A3934 " ideal model delta sigma weight residual 1.522 1.361 0.161 1.37e-02 5.33e+03 1.38e+02 bond pdb=" CA PHE A3929 " pdb=" C PHE A3929 " ideal model delta sigma weight residual 1.524 1.372 0.152 1.37e-02 5.33e+03 1.23e+02 bond pdb=" CA THR A3926 " pdb=" C THR A3926 " ideal model delta sigma weight residual 1.522 1.386 0.136 1.40e-02 5.10e+03 9.48e+01 bond pdb=" CA GLU A4926 " pdb=" C GLU A4926 " ideal model delta sigma weight residual 1.523 1.402 0.120 1.35e-02 5.49e+03 7.96e+01 bond pdb=" CA LEU A3935 " pdb=" C LEU A3935 " ideal model delta sigma weight residual 1.522 1.412 0.109 1.40e-02 5.10e+03 6.07e+01 ... (remaining 11889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 15783 2.97 - 5.93: 271 5.93 - 8.90: 56 8.90 - 11.87: 11 11.87 - 14.84: 6 Bond angle restraints: 16127 Sorted by residual: angle pdb=" N SER A3939 " pdb=" CA SER A3939 " pdb=" C SER A3939 " ideal model delta sigma weight residual 111.36 96.52 14.84 1.09e+00 8.42e-01 1.85e+02 angle pdb=" N PHE A3929 " pdb=" CA PHE A3929 " pdb=" C PHE A3929 " ideal model delta sigma weight residual 112.45 99.42 13.03 1.39e+00 5.18e-01 8.79e+01 angle pdb=" N LEU A3935 " pdb=" CA LEU A3935 " pdb=" C LEU A3935 " ideal model delta sigma weight residual 112.90 101.46 11.44 1.31e+00 5.83e-01 7.63e+01 angle pdb=" N VAL A4925 " pdb=" CA VAL A4925 " pdb=" C VAL A4925 " ideal model delta sigma weight residual 110.62 119.22 -8.60 1.02e+00 9.61e-01 7.12e+01 angle pdb=" N GLU A3938 " pdb=" CA GLU A3938 " pdb=" CB GLU A3938 " ideal model delta sigma weight residual 110.73 98.50 12.23 1.55e+00 4.16e-01 6.22e+01 ... (remaining 16122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6336 17.88 - 35.75: 741 35.75 - 53.63: 182 53.63 - 71.51: 32 71.51 - 89.39: 16 Dihedral angle restraints: 7307 sinusoidal: 3025 harmonic: 4282 Sorted by residual: dihedral pdb=" N ALA A3985 " pdb=" C ALA A3985 " pdb=" CA ALA A3985 " pdb=" CB ALA A3985 " ideal model delta harmonic sigma weight residual 122.90 139.57 -16.67 0 2.50e+00 1.60e-01 4.45e+01 dihedral pdb=" CA ILE A4268 " pdb=" C ILE A4268 " pdb=" N ARG A4269 " pdb=" CA ARG A4269 " ideal model delta harmonic sigma weight residual 180.00 148.87 31.13 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" C ALA A3985 " pdb=" N ALA A3985 " pdb=" CA ALA A3985 " pdb=" CB ALA A3985 " ideal model delta harmonic sigma weight residual -122.60 -137.83 15.23 0 2.50e+00 1.60e-01 3.71e+01 ... (remaining 7304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1801 0.161 - 0.322: 30 0.322 - 0.482: 6 0.482 - 0.643: 1 0.643 - 0.804: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" CA ALA A3985 " pdb=" N ALA A3985 " pdb=" C ALA A3985 " pdb=" CB ALA A3985 " both_signs ideal model delta sigma weight residual False 2.48 1.68 0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA ASN A4936 " pdb=" N ASN A4936 " pdb=" C ASN A4936 " pdb=" CB ASN A4936 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA VAL A4925 " pdb=" N VAL A4925 " pdb=" C VAL A4925 " pdb=" CB VAL A4925 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 1837 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A3972 " -0.048 2.00e-02 2.50e+03 9.24e-02 8.54e+01 pdb=" C GLU A3972 " 0.160 2.00e-02 2.50e+03 pdb=" O GLU A3972 " -0.059 2.00e-02 2.50e+03 pdb=" N ALA A3973 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A4930 " 0.079 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO A4931 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A4931 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A4931 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A3988 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C THR A3988 " -0.078 2.00e-02 2.50e+03 pdb=" O THR A3988 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A3989 " 0.027 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 131 2.59 - 3.17: 10068 3.17 - 3.74: 18276 3.74 - 4.32: 24553 4.32 - 4.90: 39582 Nonbonded interactions: 92610 Sorted by model distance: nonbonded pdb=" N GLU A3938 " pdb=" CG GLU A3938 " model vdw 2.010 2.816 nonbonded pdb=" O ASP A4440 " pdb=" OG1 THR A4444 " model vdw 2.039 3.040 nonbonded pdb=" O ALA A4023 " pdb=" OG SER A4027 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR A4362 " pdb=" OE1 GLN A4367 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP A3964 " pdb=" OG1 THR A3967 " model vdw 2.204 3.040 ... (remaining 92605 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 11.690 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.161 11894 Z= 0.501 Angle : 0.991 14.837 16127 Z= 0.598 Chirality : 0.063 0.804 1840 Planarity : 0.007 0.119 2080 Dihedral : 16.672 89.386 4505 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.96 % Favored : 90.62 % Rotamer: Outliers : 1.68 % Allowed : 16.53 % Favored : 81.79 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.22), residues: 1440 helix: -0.18 (0.20), residues: 741 sheet: -2.17 (0.75), residues: 52 loop : -1.98 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4970 TYR 0.019 0.002 TYR A4923 PHE 0.022 0.002 PHE A4951 TRP 0.009 0.001 TRP A3723 HIS 0.008 0.001 HIS A3932 Details of bonding type rmsd covalent geometry : bond 0.00744 (11894) covalent geometry : angle 0.99146 (16127) hydrogen bonds : bond 0.17466 ( 519) hydrogen bonds : angle 6.91848 ( 1521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.4859 (tm-30) cc_final: 0.3656 (tt0) REVERT: A 3940 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7446 (tmt170) REVERT: A 4866 PHE cc_start: 0.8840 (t80) cc_final: 0.8582 (t80) REVERT: A 4926 GLU cc_start: 0.7875 (tt0) cc_final: 0.7655 (tt0) REVERT: A 4952 ASP cc_start: 0.7562 (t0) cc_final: 0.7183 (t70) REVERT: A 4974 LYS cc_start: 0.6007 (mtmm) cc_final: 0.5756 (mttt) outliers start: 22 outliers final: 9 residues processed: 164 average time/residue: 0.1073 time to fit residues: 25.4348 Evaluate side-chains 139 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3933 VAL Chi-restraints excluded: chain A residue 3935 LEU Chi-restraints excluded: chain A residue 3938 GLU Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 3981 CYS Chi-restraints excluded: chain A residue 4061 PHE Chi-restraints excluded: chain A residue 4284 SER Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4924 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0070 chunk 55 optimal weight: 20.0000 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN A4016 HIS A4063 GLN A4121 ASN ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.166745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116854 restraints weight = 22211.422| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.89 r_work: 0.3495 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11894 Z= 0.136 Angle : 0.690 9.984 16127 Z= 0.344 Chirality : 0.043 0.327 1840 Planarity : 0.006 0.056 2080 Dihedral : 6.229 56.732 1582 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.61 % Favored : 91.25 % Rotamer: Outliers : 2.45 % Allowed : 15.68 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.22), residues: 1440 helix: 0.06 (0.19), residues: 753 sheet: -1.95 (0.80), residues: 48 loop : -1.94 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A4970 TYR 0.012 0.001 TYR A3818 PHE 0.019 0.002 PHE A4812 TRP 0.007 0.001 TRP A3723 HIS 0.008 0.001 HIS A4113 Details of bonding type rmsd covalent geometry : bond 0.00307 (11894) covalent geometry : angle 0.69005 (16127) hydrogen bonds : bond 0.05040 ( 519) hydrogen bonds : angle 4.93742 ( 1521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.5382 (tm-30) cc_final: 0.4356 (mt-10) REVERT: A 3919 GLN cc_start: 0.8904 (mt0) cc_final: 0.8684 (mp10) REVERT: A 3940 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7940 (tmt170) REVERT: A 3964 ASP cc_start: 0.8339 (t70) cc_final: 0.8049 (t0) REVERT: A 4327 TYR cc_start: 0.8675 (m-80) cc_final: 0.8373 (m-80) REVERT: A 4673 MET cc_start: 0.8120 (mmt) cc_final: 0.7919 (mmt) REVERT: A 4866 PHE cc_start: 0.8938 (t80) cc_final: 0.8519 (t80) outliers start: 32 outliers final: 13 residues processed: 175 average time/residue: 0.1084 time to fit residues: 27.8970 Evaluate side-chains 145 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3898 SER Chi-restraints excluded: chain A residue 3933 VAL Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4073 VAL Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4324 MET Chi-restraints excluded: chain A residue 4468 LEU Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4838 LYS Chi-restraints excluded: chain A residue 4843 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 1 optimal weight: 0.0020 chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 46 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.165217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116465 restraints weight = 22451.076| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.62 r_work: 0.3472 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11894 Z= 0.146 Angle : 0.661 9.884 16127 Z= 0.332 Chirality : 0.042 0.204 1840 Planarity : 0.005 0.051 2080 Dihedral : 5.574 53.977 1568 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.19 % Favored : 91.67 % Rotamer: Outliers : 2.75 % Allowed : 16.60 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.22), residues: 1440 helix: 0.29 (0.19), residues: 754 sheet: -1.91 (0.81), residues: 48 loop : -1.90 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4970 TYR 0.013 0.001 TYR A3818 PHE 0.020 0.002 PHE A3751 TRP 0.008 0.001 TRP A3792 HIS 0.008 0.001 HIS A4113 Details of bonding type rmsd covalent geometry : bond 0.00345 (11894) covalent geometry : angle 0.66123 (16127) hydrogen bonds : bond 0.04338 ( 519) hydrogen bonds : angle 4.60166 ( 1521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.5375 (tm-30) cc_final: 0.4328 (mt-10) REVERT: A 3964 ASP cc_start: 0.8391 (t70) cc_final: 0.8045 (t0) REVERT: A 3975 MET cc_start: 0.8478 (mtp) cc_final: 0.8240 (mtm) REVERT: A 4327 TYR cc_start: 0.8749 (m-80) cc_final: 0.8460 (m-80) REVERT: A 4673 MET cc_start: 0.8112 (mmt) cc_final: 0.7668 (mmt) REVERT: A 4855 TYR cc_start: 0.7499 (m-80) cc_final: 0.6778 (m-80) REVERT: A 4945 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5779 (mpp80) REVERT: A 4952 ASP cc_start: 0.7675 (t0) cc_final: 0.7459 (t0) outliers start: 36 outliers final: 20 residues processed: 168 average time/residue: 0.1083 time to fit residues: 26.3386 Evaluate side-chains 150 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3935 LEU Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 3967 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4073 VAL Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4195 LEU Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4619 HIS Chi-restraints excluded: chain A residue 4778 LEU Chi-restraints excluded: chain A residue 4790 LEU Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4801 VAL Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4900 LYS Chi-restraints excluded: chain A residue 4916 THR Chi-restraints excluded: chain A residue 4945 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN A3919 GLN ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.164963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115976 restraints weight = 22234.907| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.71 r_work: 0.3465 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11894 Z= 0.139 Angle : 0.657 12.054 16127 Z= 0.324 Chirality : 0.043 0.352 1840 Planarity : 0.005 0.055 2080 Dihedral : 5.484 58.958 1567 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.40 % Favored : 91.46 % Rotamer: Outliers : 3.52 % Allowed : 17.52 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.22), residues: 1440 helix: 0.34 (0.19), residues: 768 sheet: -1.85 (0.82), residues: 48 loop : -1.83 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4060 TYR 0.012 0.001 TYR A3818 PHE 0.020 0.002 PHE A4866 TRP 0.008 0.001 TRP A3792 HIS 0.006 0.001 HIS A4113 Details of bonding type rmsd covalent geometry : bond 0.00330 (11894) covalent geometry : angle 0.65657 (16127) hydrogen bonds : bond 0.03952 ( 519) hydrogen bonds : angle 4.41441 ( 1521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.5542 (tm-30) cc_final: 0.4674 (mt-10) REVERT: A 3964 ASP cc_start: 0.8339 (t70) cc_final: 0.7941 (t0) REVERT: A 3972 GLU cc_start: 0.8207 (mp0) cc_final: 0.7987 (tp30) REVERT: A 3989 LEU cc_start: 0.8357 (mt) cc_final: 0.8155 (pp) REVERT: A 4189 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6493 (m-10) REVERT: A 4327 TYR cc_start: 0.8739 (m-80) cc_final: 0.8415 (m-80) REVERT: A 4644 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 4673 MET cc_start: 0.8168 (mmt) cc_final: 0.7598 (mmt) REVERT: A 4855 TYR cc_start: 0.7487 (m-80) cc_final: 0.7164 (m-80) REVERT: A 4945 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.5814 (mpp80) outliers start: 46 outliers final: 27 residues processed: 175 average time/residue: 0.1107 time to fit residues: 28.1076 Evaluate side-chains 159 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3768 LEU Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3899 ASP Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4051 HIS Chi-restraints excluded: chain A residue 4057 LYS Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4073 VAL Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4189 TYR Chi-restraints excluded: chain A residue 4195 LEU Chi-restraints excluded: chain A residue 4324 MET Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4619 HIS Chi-restraints excluded: chain A residue 4644 LEU Chi-restraints excluded: chain A residue 4778 LEU Chi-restraints excluded: chain A residue 4790 LEU Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4801 VAL Chi-restraints excluded: chain A residue 4838 LYS Chi-restraints excluded: chain A residue 4894 ILE Chi-restraints excluded: chain A residue 4900 LYS Chi-restraints excluded: chain A residue 4941 VAL Chi-restraints excluded: chain A residue 4945 ARG Chi-restraints excluded: chain A residue 4974 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 109 optimal weight: 0.0060 chunk 75 optimal weight: 0.5980 chunk 126 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN ** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.166394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116730 restraints weight = 22273.446| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.98 r_work: 0.3483 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11894 Z= 0.121 Angle : 0.639 14.243 16127 Z= 0.314 Chirality : 0.042 0.403 1840 Planarity : 0.005 0.053 2080 Dihedral : 5.351 54.725 1567 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.12 % Favored : 91.81 % Rotamer: Outliers : 3.21 % Allowed : 19.05 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.22), residues: 1440 helix: 0.48 (0.19), residues: 768 sheet: -2.05 (0.79), residues: 51 loop : -1.83 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4384 TYR 0.011 0.001 TYR A4896 PHE 0.030 0.001 PHE A4306 TRP 0.008 0.001 TRP A3792 HIS 0.005 0.001 HIS A4113 Details of bonding type rmsd covalent geometry : bond 0.00277 (11894) covalent geometry : angle 0.63947 (16127) hydrogen bonds : bond 0.03698 ( 519) hydrogen bonds : angle 4.26423 ( 1521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.2118 (OUTLIER) cc_final: 0.1776 (mpt) REVERT: B 172 GLU cc_start: 0.5613 (tm-30) cc_final: 0.4784 (mt-10) REVERT: A 3720 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 3919 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8539 (mp10) REVERT: A 3945 GLN cc_start: 0.6907 (tp-100) cc_final: 0.6694 (tp40) REVERT: A 3964 ASP cc_start: 0.8265 (t70) cc_final: 0.7862 (t0) REVERT: A 4064 MET cc_start: 0.7736 (mpp) cc_final: 0.7509 (mpp) REVERT: A 4327 TYR cc_start: 0.8693 (m-80) cc_final: 0.8383 (m-80) REVERT: A 4673 MET cc_start: 0.8180 (mmt) cc_final: 0.7521 (mmt) REVERT: A 4802 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.6740 (tp40) REVERT: A 4812 PHE cc_start: 0.7952 (t80) cc_final: 0.7630 (t80) REVERT: A 4855 TYR cc_start: 0.7465 (m-80) cc_final: 0.6551 (m-80) REVERT: A 4945 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5870 (mpp80) REVERT: A 4952 ASP cc_start: 0.7671 (t0) cc_final: 0.7068 (t0) outliers start: 42 outliers final: 27 residues processed: 170 average time/residue: 0.1139 time to fit residues: 27.8924 Evaluate side-chains 159 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3839 LEU Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3899 ASP Chi-restraints excluded: chain A residue 3919 GLN Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 3967 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4051 HIS Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4195 LEU Chi-restraints excluded: chain A residue 4324 MET Chi-restraints excluded: chain A residue 4351 LEU Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4619 HIS Chi-restraints excluded: chain A residue 4778 LEU Chi-restraints excluded: chain A residue 4790 LEU Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4801 VAL Chi-restraints excluded: chain A residue 4802 GLN Chi-restraints excluded: chain A residue 4838 LYS Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4894 ILE Chi-restraints excluded: chain A residue 4900 LYS Chi-restraints excluded: chain A residue 4941 VAL Chi-restraints excluded: chain A residue 4945 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 98 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN ** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.165947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.116715 restraints weight = 22369.731| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.66 r_work: 0.3477 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11894 Z= 0.128 Angle : 0.643 10.747 16127 Z= 0.316 Chirality : 0.043 0.373 1840 Planarity : 0.005 0.054 2080 Dihedral : 5.264 49.424 1567 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 3.90 % Allowed : 18.82 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.22), residues: 1440 helix: 0.54 (0.19), residues: 769 sheet: -2.02 (0.79), residues: 51 loop : -1.77 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4927 TYR 0.019 0.001 TYR A4189 PHE 0.025 0.001 PHE A4306 TRP 0.007 0.001 TRP A3723 HIS 0.003 0.001 HIS A4113 Details of bonding type rmsd covalent geometry : bond 0.00307 (11894) covalent geometry : angle 0.64280 (16127) hydrogen bonds : bond 0.03668 ( 519) hydrogen bonds : angle 4.17054 ( 1521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.2048 (OUTLIER) cc_final: 0.1582 (mpt) REVERT: B 172 GLU cc_start: 0.5536 (tm-30) cc_final: 0.4677 (mt-10) REVERT: A 3915 GLU cc_start: 0.8839 (tp30) cc_final: 0.8443 (tp30) REVERT: A 3919 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8172 (mp-120) REVERT: A 3945 GLN cc_start: 0.6925 (tp-100) cc_final: 0.5425 (tp-100) REVERT: A 3964 ASP cc_start: 0.8287 (t70) cc_final: 0.7887 (t0) REVERT: A 4064 MET cc_start: 0.7904 (mpp) cc_final: 0.7561 (mpp) REVERT: A 4327 TYR cc_start: 0.8734 (m-80) cc_final: 0.8433 (m-80) REVERT: A 4621 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8755 (mp) REVERT: A 4644 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8581 (mp) REVERT: A 4673 MET cc_start: 0.8223 (mmt) cc_final: 0.7552 (mmt) REVERT: A 4802 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6752 (tp40) REVERT: A 4812 PHE cc_start: 0.8013 (t80) cc_final: 0.7740 (t80) REVERT: A 4855 TYR cc_start: 0.7392 (m-80) cc_final: 0.6476 (m-80) REVERT: A 4945 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.5970 (mpp80) REVERT: A 4952 ASP cc_start: 0.7624 (t0) cc_final: 0.6884 (t0) outliers start: 51 outliers final: 34 residues processed: 178 average time/residue: 0.1067 time to fit residues: 27.3864 Evaluate side-chains 169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3891 MET Chi-restraints excluded: chain A residue 3899 ASP Chi-restraints excluded: chain A residue 3919 GLN Chi-restraints excluded: chain A residue 3933 VAL Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 3967 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4057 LYS Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4061 PHE Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4195 LEU Chi-restraints excluded: chain A residue 4324 MET Chi-restraints excluded: chain A residue 4351 LEU Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4619 HIS Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4644 LEU Chi-restraints excluded: chain A residue 4778 LEU Chi-restraints excluded: chain A residue 4790 LEU Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4801 VAL Chi-restraints excluded: chain A residue 4802 GLN Chi-restraints excluded: chain A residue 4838 LYS Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4894 ILE Chi-restraints excluded: chain A residue 4900 LYS Chi-restraints excluded: chain A residue 4903 LYS Chi-restraints excluded: chain A residue 4910 VAL Chi-restraints excluded: chain A residue 4916 THR Chi-restraints excluded: chain A residue 4941 VAL Chi-restraints excluded: chain A residue 4945 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN ** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3945 GLN ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.161241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111353 restraints weight = 22399.310| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.75 r_work: 0.3397 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11894 Z= 0.225 Angle : 0.730 11.152 16127 Z= 0.361 Chirality : 0.045 0.279 1840 Planarity : 0.005 0.051 2080 Dihedral : 5.410 43.555 1567 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.24 % Favored : 90.62 % Rotamer: Outliers : 4.59 % Allowed : 18.82 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.22), residues: 1440 helix: 0.32 (0.19), residues: 780 sheet: -1.92 (0.82), residues: 49 loop : -1.77 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4970 TYR 0.016 0.002 TYR A3818 PHE 0.030 0.002 PHE A4306 TRP 0.007 0.001 TRP A3723 HIS 0.005 0.001 HIS A4113 Details of bonding type rmsd covalent geometry : bond 0.00542 (11894) covalent geometry : angle 0.73010 (16127) hydrogen bonds : bond 0.04122 ( 519) hydrogen bonds : angle 4.40688 ( 1521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 MET cc_start: 0.2012 (OUTLIER) cc_final: 0.1662 (mpt) REVERT: B 172 GLU cc_start: 0.5570 (tm-30) cc_final: 0.4777 (mt-10) REVERT: A 3919 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8608 (mp10) REVERT: A 3940 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8190 (tmt170) REVERT: A 4068 PHE cc_start: 0.8166 (m-10) cc_final: 0.7761 (m-10) REVERT: A 4621 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8831 (mp) REVERT: A 4644 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 4673 MET cc_start: 0.8328 (mmt) cc_final: 0.7604 (mmt) REVERT: A 4802 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: A 4812 PHE cc_start: 0.8142 (t80) cc_final: 0.7818 (t80) REVERT: A 4943 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7013 (tp30) REVERT: A 4945 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6101 (mpp80) REVERT: A 4952 ASP cc_start: 0.7749 (t0) cc_final: 0.7023 (t0) outliers start: 60 outliers final: 39 residues processed: 173 average time/residue: 0.1089 time to fit residues: 27.5270 Evaluate side-chains 171 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3768 LEU Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3780 THR Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3891 MET Chi-restraints excluded: chain A residue 3899 ASP Chi-restraints excluded: chain A residue 3919 GLN Chi-restraints excluded: chain A residue 3933 VAL Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 3967 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4057 LYS Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4061 PHE Chi-restraints excluded: chain A residue 4073 VAL Chi-restraints excluded: chain A residue 4133 VAL Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4195 LEU Chi-restraints excluded: chain A residue 4260 LEU Chi-restraints excluded: chain A residue 4351 LEU Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4559 LEU Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4644 LEU Chi-restraints excluded: chain A residue 4778 LEU Chi-restraints excluded: chain A residue 4790 LEU Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4801 VAL Chi-restraints excluded: chain A residue 4802 GLN Chi-restraints excluded: chain A residue 4838 LYS Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4894 ILE Chi-restraints excluded: chain A residue 4900 LYS Chi-restraints excluded: chain A residue 4903 LYS Chi-restraints excluded: chain A residue 4910 VAL Chi-restraints excluded: chain A residue 4916 THR Chi-restraints excluded: chain A residue 4941 VAL Chi-restraints excluded: chain A residue 4943 GLU Chi-restraints excluded: chain A residue 4945 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 0.3980 chunk 136 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN ** A3827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3945 GLN ** A4293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.161359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.112508 restraints weight = 21652.731| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.61 r_work: 0.3377 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11894 Z= 0.133 Angle : 0.667 11.124 16127 Z= 0.329 Chirality : 0.043 0.231 1840 Planarity : 0.005 0.056 2080 Dihedral : 5.358 38.729 1567 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.33 % Favored : 91.60 % Rotamer: Outliers : 3.98 % Allowed : 19.05 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.22), residues: 1440 helix: 0.52 (0.19), residues: 767 sheet: -2.05 (0.79), residues: 51 loop : -1.70 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4970 TYR 0.014 0.001 TYR A4189 PHE 0.024 0.001 PHE A4306 TRP 0.009 0.001 TRP A3792 HIS 0.008 0.001 HIS A4619 Details of bonding type rmsd covalent geometry : bond 0.00320 (11894) covalent geometry : angle 0.66675 (16127) hydrogen bonds : bond 0.03792 ( 519) hydrogen bonds : angle 4.21652 ( 1521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.5488 (tm-30) cc_final: 0.4705 (mt-10) REVERT: A 3796 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8312 (ttp-110) REVERT: A 3915 GLU cc_start: 0.8753 (tp30) cc_final: 0.8358 (tp30) REVERT: A 3919 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8065 (mp-120) REVERT: A 4068 PHE cc_start: 0.8185 (m-10) cc_final: 0.7713 (m-10) REVERT: A 4327 TYR cc_start: 0.8755 (m-80) cc_final: 0.8440 (m-80) REVERT: A 4621 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 4644 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8555 (mp) REVERT: A 4673 MET cc_start: 0.8166 (mmt) cc_final: 0.7461 (mmt) REVERT: A 4802 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6762 (tp40) REVERT: A 4943 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: A 4945 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.5922 (mpp80) REVERT: A 4952 ASP cc_start: 0.7570 (t0) cc_final: 0.6804 (t0) outliers start: 52 outliers final: 36 residues processed: 168 average time/residue: 0.1105 time to fit residues: 26.7694 Evaluate side-chains 168 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3796 ARG Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3891 MET Chi-restraints excluded: chain A residue 3899 ASP Chi-restraints excluded: chain A residue 3919 GLN Chi-restraints excluded: chain A residue 3933 VAL Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 3967 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4057 LYS Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4061 PHE Chi-restraints excluded: chain A residue 4144 HIS Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4195 LEU Chi-restraints excluded: chain A residue 4260 LEU Chi-restraints excluded: chain A residue 4324 MET Chi-restraints excluded: chain A residue 4351 LEU Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4619 HIS Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4644 LEU Chi-restraints excluded: chain A residue 4778 LEU Chi-restraints excluded: chain A residue 4790 LEU Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4801 VAL Chi-restraints excluded: chain A residue 4802 GLN Chi-restraints excluded: chain A residue 4838 LYS Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4894 ILE Chi-restraints excluded: chain A residue 4903 LYS Chi-restraints excluded: chain A residue 4916 THR Chi-restraints excluded: chain A residue 4941 VAL Chi-restraints excluded: chain A residue 4943 GLU Chi-restraints excluded: chain A residue 4945 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 67 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 0.0170 chunk 133 optimal weight: 0.1980 chunk 123 optimal weight: 0.0770 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN A3827 ASN ** A3945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.163632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114946 restraints weight = 21303.867| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.68 r_work: 0.3418 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11894 Z= 0.117 Angle : 0.648 11.252 16127 Z= 0.319 Chirality : 0.042 0.215 1840 Planarity : 0.005 0.058 2080 Dihedral : 5.187 41.600 1567 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.99 % Favored : 91.94 % Rotamer: Outliers : 3.44 % Allowed : 20.20 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.23), residues: 1440 helix: 0.70 (0.19), residues: 767 sheet: -1.96 (0.81), residues: 50 loop : -1.64 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4970 TYR 0.013 0.001 TYR A4189 PHE 0.014 0.001 PHE A4403 TRP 0.010 0.001 TRP A3792 HIS 0.007 0.001 HIS A3951 Details of bonding type rmsd covalent geometry : bond 0.00279 (11894) covalent geometry : angle 0.64841 (16127) hydrogen bonds : bond 0.03587 ( 519) hydrogen bonds : angle 4.10353 ( 1521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3796 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8254 (ttp-110) REVERT: A 3915 GLU cc_start: 0.8734 (tp30) cc_final: 0.8363 (tp30) REVERT: A 3919 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8073 (mp-120) REVERT: A 4057 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.6758 (pttt) REVERT: A 4068 PHE cc_start: 0.8191 (m-10) cc_final: 0.7816 (m-10) REVERT: A 4151 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8240 (tt0) REVERT: A 4327 TYR cc_start: 0.8697 (m-80) cc_final: 0.8392 (m-80) REVERT: A 4371 PHE cc_start: 0.8042 (t80) cc_final: 0.7402 (t80) REVERT: A 4621 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 4644 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8506 (mp) REVERT: A 4652 GLU cc_start: 0.7440 (tp30) cc_final: 0.7118 (tp30) REVERT: A 4673 MET cc_start: 0.8102 (mmt) cc_final: 0.7411 (mmt) REVERT: A 4802 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.6787 (tp40) REVERT: A 4945 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.5895 (mpp80) REVERT: A 4952 ASP cc_start: 0.7538 (t0) cc_final: 0.6822 (t0) outliers start: 45 outliers final: 31 residues processed: 176 average time/residue: 0.1193 time to fit residues: 30.2676 Evaluate side-chains 169 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3774 LEU Chi-restraints excluded: chain A residue 3796 ARG Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3891 MET Chi-restraints excluded: chain A residue 3899 ASP Chi-restraints excluded: chain A residue 3919 GLN Chi-restraints excluded: chain A residue 3933 VAL Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 3967 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4057 LYS Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4061 PHE Chi-restraints excluded: chain A residue 4144 HIS Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4195 LEU Chi-restraints excluded: chain A residue 4260 LEU Chi-restraints excluded: chain A residue 4324 MET Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4440 ASP Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4619 HIS Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4644 LEU Chi-restraints excluded: chain A residue 4790 LEU Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4801 VAL Chi-restraints excluded: chain A residue 4802 GLN Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4894 ILE Chi-restraints excluded: chain A residue 4941 VAL Chi-restraints excluded: chain A residue 4945 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.0030 chunk 9 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN ** A3945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.163756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114371 restraints weight = 21831.397| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.88 r_work: 0.3412 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11894 Z= 0.120 Angle : 0.687 16.654 16127 Z= 0.330 Chirality : 0.043 0.438 1840 Planarity : 0.005 0.058 2080 Dihedral : 5.137 42.147 1567 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.92 % Favored : 92.01 % Rotamer: Outliers : 3.06 % Allowed : 20.96 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.23), residues: 1440 helix: 0.74 (0.19), residues: 767 sheet: -1.94 (0.81), residues: 50 loop : -1.61 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4970 TYR 0.014 0.001 TYR A4189 PHE 0.027 0.001 PHE A4306 TRP 0.014 0.001 TRP A3792 HIS 0.007 0.001 HIS A3951 Details of bonding type rmsd covalent geometry : bond 0.00289 (11894) covalent geometry : angle 0.68726 (16127) hydrogen bonds : bond 0.03603 ( 519) hydrogen bonds : angle 4.11979 ( 1521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.6040 (tm-30) cc_final: 0.5003 (mt-10) REVERT: A 3796 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8168 (mtm-85) REVERT: A 3915 GLU cc_start: 0.8757 (tp30) cc_final: 0.8391 (tp30) REVERT: A 3919 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8112 (mp-120) REVERT: A 4057 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.6812 (pttt) REVERT: A 4068 PHE cc_start: 0.8294 (m-10) cc_final: 0.7855 (m-10) REVERT: A 4151 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8199 (tt0) REVERT: A 4327 TYR cc_start: 0.8705 (m-80) cc_final: 0.8400 (m-80) REVERT: A 4621 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8638 (mp) REVERT: A 4644 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8469 (mp) REVERT: A 4673 MET cc_start: 0.8111 (mmt) cc_final: 0.7423 (mmt) REVERT: A 4802 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6838 (tp40) REVERT: A 4866 PHE cc_start: 0.8468 (t80) cc_final: 0.8154 (t80) REVERT: A 4945 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.5908 (mpp80) REVERT: A 4952 ASP cc_start: 0.7559 (t0) cc_final: 0.6848 (t0) outliers start: 40 outliers final: 29 residues processed: 160 average time/residue: 0.1140 time to fit residues: 26.6600 Evaluate side-chains 165 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain A residue 3728 TYR Chi-restraints excluded: chain A residue 3730 THR Chi-restraints excluded: chain A residue 3796 ARG Chi-restraints excluded: chain A residue 3869 MET Chi-restraints excluded: chain A residue 3891 MET Chi-restraints excluded: chain A residue 3899 ASP Chi-restraints excluded: chain A residue 3919 GLN Chi-restraints excluded: chain A residue 3933 VAL Chi-restraints excluded: chain A residue 3940 ARG Chi-restraints excluded: chain A residue 3967 THR Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4057 LYS Chi-restraints excluded: chain A residue 4058 HIS Chi-restraints excluded: chain A residue 4061 PHE Chi-restraints excluded: chain A residue 4144 HIS Chi-restraints excluded: chain A residue 4164 THR Chi-restraints excluded: chain A residue 4195 LEU Chi-restraints excluded: chain A residue 4260 LEU Chi-restraints excluded: chain A residue 4324 MET Chi-restraints excluded: chain A residue 4362 THR Chi-restraints excluded: chain A residue 4440 ASP Chi-restraints excluded: chain A residue 4609 VAL Chi-restraints excluded: chain A residue 4619 HIS Chi-restraints excluded: chain A residue 4621 LEU Chi-restraints excluded: chain A residue 4644 LEU Chi-restraints excluded: chain A residue 4790 LEU Chi-restraints excluded: chain A residue 4800 ASN Chi-restraints excluded: chain A residue 4802 GLN Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4894 ILE Chi-restraints excluded: chain A residue 4941 VAL Chi-restraints excluded: chain A residue 4945 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 94 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3727 GLN ** A3945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4261 GLN ** A4587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4654 HIS A4826 HIS ** A4936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.160053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111023 restraints weight = 21774.817| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.79 r_work: 0.3345 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11894 Z= 0.180 Angle : 0.723 15.422 16127 Z= 0.349 Chirality : 0.045 0.449 1840 Planarity : 0.005 0.054 2080 Dihedral : 5.230 40.868 1567 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.82 % Favored : 91.04 % Rotamer: Outliers : 3.14 % Allowed : 20.96 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.23), residues: 1440 helix: 0.66 (0.19), residues: 767 sheet: -1.98 (0.81), residues: 50 loop : -1.64 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4231 TYR 0.014 0.001 TYR A4189 PHE 0.026 0.002 PHE A4306 TRP 0.013 0.001 TRP A4304 HIS 0.006 0.001 HIS A4619 Details of bonding type rmsd covalent geometry : bond 0.00436 (11894) covalent geometry : angle 0.72299 (16127) hydrogen bonds : bond 0.03869 ( 519) hydrogen bonds : angle 4.26241 ( 1521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3730.58 seconds wall clock time: 64 minutes 40.68 seconds (3880.68 seconds total)