Starting phenix.real_space_refine on Tue Aug 4 14:56:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j7r_36046/08_2026/8j7r_36046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7r_36046/08_2026/8j7r_36046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j7r_36046/08_2026/8j7r_36046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7r_36046/08_2026/8j7r_36046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j7r_36046/08_2026/8j7r_36046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7r_36046/08_2026/8j7r_36046.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8j7r_36046/08_2026/8j7r_36046.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j7r_36046/08_2026/8j7r_36046.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 97 5.49 5 Mg 3 5.21 5 S 16 5.16 5 C 2154 2.51 5 N 721 2.21 5 O 1043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4034 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1951 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain: "C" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2079 Classifications: {'RNAv2': 97} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 2, 'rna3p_pur': 43, 'rna3p_pyr': 41} Link IDs: {'rna2p': 13, 'rna3p': 83} Chain breaks: 2 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 1.30, per 1000 atoms: 0.32 Number of scatterers: 4034 At special positions: 0 Unit cell: (100.98, 91.8, 84.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 P 97 15.00 Mg 3 11.99 O 1043 8.00 N 721 7.00 C 2154 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: 0.36 Conformation dependent library (CDL) restraints added in 98.8 milliseconds 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 462 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 85.7% alpha, 0.8% beta 37 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'B' and resid 754 through 771 removed outlier: 3.874A pdb=" N GLN B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 785 removed outlier: 3.724A pdb=" N LEU B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 808 Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.560A pdb=" N LEU B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 852 Processing helix chain 'B' and resid 853 through 871 removed outlier: 3.764A pdb=" N ASP B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 908 removed outlier: 3.544A pdb=" N LEU B 908 " --> pdb=" O GLU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 removed outlier: 3.598A pdb=" N MET B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 921 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 922 " --> pdb=" O ASP B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 947 removed outlier: 6.050A pdb=" N LYS B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP B 945 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 951 through 969 removed outlier: 3.535A pdb=" N PHE B 959 " --> pdb=" O MET B 955 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 960 " --> pdb=" O ASP B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 988 Processing sheet with id=AA1, first strand: chain 'B' and resid 827 through 828 140 hydrogen bonds defined for protein. 417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 914 1.34 - 1.46: 1387 1.46 - 1.58: 1779 1.58 - 1.71: 191 1.71 - 1.83: 26 Bond restraints: 4297 Sorted by residual: bond pdb=" N ILE B 942 " pdb=" CA ILE B 942 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.90e+00 bond pdb=" N GLU B 852 " pdb=" CA GLU B 852 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.40e+00 bond pdb=" CA SER B 812 " pdb=" CB SER B 812 " ideal model delta sigma weight residual 1.529 1.488 0.041 1.58e-02 4.01e+03 6.88e+00 bond pdb=" N VAL B 835 " pdb=" CA VAL B 835 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.32e-02 5.74e+03 6.77e+00 bond pdb=" N LYS B 756 " pdb=" CA LYS B 756 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.21e+00 ... (remaining 4292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 4516 1.41 - 2.82: 1374 2.82 - 4.23: 280 4.23 - 5.64: 74 5.64 - 7.05: 8 Bond angle restraints: 6252 Sorted by residual: angle pdb=" CA PHE B 839 " pdb=" CB PHE B 839 " pdb=" CG PHE B 839 " ideal model delta sigma weight residual 113.80 118.40 -4.60 1.00e+00 1.00e+00 2.12e+01 angle pdb=" CA VAL B 835 " pdb=" C VAL B 835 " pdb=" O VAL B 835 " ideal model delta sigma weight residual 121.92 117.43 4.49 1.17e+00 7.31e-01 1.47e+01 angle pdb=" C3' U C 778 " pdb=" O3' U C 778 " pdb=" P C C 779 " ideal model delta sigma weight residual 119.70 124.25 -4.55 1.20e+00 6.94e-01 1.44e+01 angle pdb=" N ARG B 892 " pdb=" CA ARG B 892 " pdb=" C ARG B 892 " ideal model delta sigma weight residual 111.82 107.65 4.17 1.16e+00 7.43e-01 1.29e+01 angle pdb=" C ALA B 805 " pdb=" N ILE B 806 " pdb=" CA ILE B 806 " ideal model delta sigma weight residual 121.55 116.57 4.98 1.42e+00 4.96e-01 1.23e+01 ... (remaining 6247 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 31.70: 2083 31.70 - 63.39: 302 63.39 - 95.08: 27 95.08 - 126.77: 0 126.77 - 158.46: 1 Dihedral angle restraints: 2413 sinusoidal: 1712 harmonic: 701 Sorted by residual: dihedral pdb=" C4' G C 777 " pdb=" C3' G C 777 " pdb=" C2' G C 777 " pdb=" C1' G C 777 " ideal model delta sinusoidal sigma weight residual 36.35 -42.25 78.60 1 3.10e+00 1.04e-01 8.01e+02 dihedral pdb=" C4' A C 775 " pdb=" C3' A C 775 " pdb=" C2' A C 775 " pdb=" C1' A C 775 " ideal model delta sinusoidal sigma weight residual 36.34 -38.59 74.94 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" C4' U C 713 " pdb=" C3' U C 713 " pdb=" C2' U C 713 " pdb=" C1' U C 713 " ideal model delta sinusoidal sigma weight residual 36.35 -37.94 74.28 1 3.10e+00 1.04e-01 7.28e+02 ... (remaining 2410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 575 0.157 - 0.313: 110 0.313 - 0.470: 45 0.470 - 0.627: 49 0.627 - 0.783: 3 Chirality restraints: 782 Sorted by residual: chirality pdb=" P C C 751 " pdb=" OP1 C C 751 " pdb=" OP2 C C 751 " pdb=" O5' C C 751 " both_signs ideal model delta sigma weight residual True 2.17 -2.96 -0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" P G C 682 " pdb=" OP1 G C 682 " pdb=" OP2 G C 682 " pdb=" O5' G C 682 " both_signs ideal model delta sigma weight residual True 2.17 2.93 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" P A C 760 " pdb=" OP1 A C 760 " pdb=" OP2 A C 760 " pdb=" O5' A C 760 " both_signs ideal model delta sigma weight residual True 2.17 2.93 -0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 779 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 839 " -0.023 2.00e-02 2.50e+03 1.62e-02 4.59e+00 pdb=" CG PHE B 839 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 839 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 839 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 839 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 839 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 839 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 704 " 0.029 2.00e-02 2.50e+03 1.19e-02 3.90e+00 pdb=" N9 A C 704 " -0.014 2.00e-02 2.50e+03 pdb=" C8 A C 704 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A C 704 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A C 704 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 704 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A C 704 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A C 704 " 0.008 2.00e-02 2.50e+03 pdb=" C2 A C 704 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A C 704 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A C 704 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 685 " -0.023 2.00e-02 2.50e+03 1.20e-02 3.22e+00 pdb=" N1 U C 685 " 0.025 2.00e-02 2.50e+03 pdb=" C2 U C 685 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U C 685 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U C 685 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U C 685 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U C 685 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U C 685 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U C 685 " 0.007 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 652 2.76 - 3.29: 3912 3.29 - 3.83: 8122 3.83 - 4.36: 9493 4.36 - 4.90: 12509 Nonbonded interactions: 34688 Sorted by model distance: nonbonded pdb=" O CYS B 936 " pdb=" OG1 THR B 940 " model vdw 2.220 3.040 nonbonded pdb=" NZ LYS B 864 " pdb=" O LEU B 880 " model vdw 2.424 3.120 nonbonded pdb=" NE2 GLN B 980 " pdb=" OD1 ASP B 984 " model vdw 2.428 3.120 nonbonded pdb=" N GLU B 859 " pdb=" OE1 GLU B 859 " model vdw 2.444 3.120 nonbonded pdb=" OE1 GLU B 968 " pdb=" NZ LYS B 970 " model vdw 2.448 3.120 ... (remaining 34683 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.010 0.041 4297 Z= 0.611 Angle : 1.410 7.052 6252 Z= 0.787 Chirality : 0.196 0.783 782 Planarity : 0.005 0.026 435 Dihedral : 23.273 158.465 1951 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 6.85 % Allowed : 23.29 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.53), residues: 236 helix: 0.49 (0.37), residues: 177 sheet: None (None), residues: 0 loop : -1.69 (0.81), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 762 TYR 0.010 0.002 TYR B 815 PHE 0.032 0.005 PHE B 839 TRP 0.009 0.003 TRP B 990 HIS 0.007 0.004 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00963 / 0.61 ( 4297) covalent geometry : angle 1.41042 / 0.79 ( 6252) hydrogen bonds : bond 0.16528 / 10.88 ( 233) hydrogen bonds : angle 6.24283 / 4.44 ( 563) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 762 ARG cc_start: 0.7668 (mmt90) cc_final: 0.6933 (tpt170) REVERT: B 775 MET cc_start: 0.8109 (tpt) cc_final: 0.7404 (ttt) REVERT: B 778 GLN cc_start: 0.8435 (mp10) cc_final: 0.8087 (mp10) REVERT: B 827 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 838 ASN cc_start: 0.8019 (t0) cc_final: 0.7774 (t0) REVERT: B 841 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7362 (tppt) REVERT: B 883 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8362 (mt-10) REVERT: B 930 GLU cc_start: 0.8070 (mp0) cc_final: 0.7662 (tt0) REVERT: B 944 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7992 (tptp) REVERT: B 949 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7915 (pt0) REVERT: B 961 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7748 (tm-30) REVERT: B 968 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 989 ASN cc_start: 0.9259 (m-40) cc_final: 0.8864 (t0) outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.0882 time to fit residues: 8.9831 Evaluate side-chains 56 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.103112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.077810 restraints weight = 10164.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080298 restraints weight = 4734.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081883 restraints weight = 3110.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082786 restraints weight = 2489.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083175 restraints weight = 2210.096| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4297 Z= 0.211 Angle : 1.133 11.017 6252 Z= 0.466 Chirality : 0.087 0.741 782 Planarity : 0.004 0.036 435 Dihedral : 19.601 161.539 1436 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 7.31 % Allowed : 26.94 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.55), residues: 236 helix: 1.50 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -1.15 (1.01), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 877 TYR 0.007 0.002 TYR B 815 PHE 0.011 0.002 PHE B 959 TRP 0.005 0.002 TRP B 990 HIS 0.002 0.001 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 ( 4297) covalent geometry : angle 1.13317 / 0.47 ( 6252) hydrogen bonds : bond 0.07493 / 5.69 ( 233) hydrogen bonds : angle 3.58702 / 2.57 ( 563) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: B 762 ARG cc_start: 0.7266 (mmt90) cc_final: 0.6998 (tpt170) REVERT: B 775 MET cc_start: 0.6381 (tpt) cc_final: 0.5769 (ttt) REVERT: B 958 TYR cc_start: 0.7725 (m-10) cc_final: 0.6660 (m-10) REVERT: B 961 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7741 (tm-30) outliers start: 16 outliers final: 9 residues processed: 55 average time/residue: 0.0778 time to fit residues: 5.2595 Evaluate side-chains 44 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 902 ILE Chi-restraints excluded: chain B residue 955 MET Chi-restraints excluded: chain B residue 961 GLN Chi-restraints excluded: chain B residue 965 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 25 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.075215 restraints weight = 10000.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077565 restraints weight = 4621.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.079105 restraints weight = 3080.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079571 restraints weight = 2478.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080273 restraints weight = 2285.357| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 4297 Z= 0.267 Angle : 1.108 9.235 6252 Z= 0.456 Chirality : 0.083 0.595 782 Planarity : 0.005 0.034 435 Dihedral : 19.327 167.976 1417 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 6.85 % Allowed : 31.05 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.56), residues: 236 helix: 1.54 (0.38), residues: 194 sheet: None (None), residues: 0 loop : -0.97 (1.03), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 893 TYR 0.005 0.002 TYR B 815 PHE 0.011 0.002 PHE B 959 TRP 0.007 0.003 TRP B 990 HIS 0.001 0.001 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.27 ( 4297) covalent geometry : angle 1.10771 / 0.46 ( 6252) hydrogen bonds : bond 0.07231 / 5.40 ( 233) hydrogen bonds : angle 3.54513 / 2.54 ( 563) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: B 762 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7008 (tpt170) REVERT: B 775 MET cc_start: 0.6499 (tpt) cc_final: 0.6075 (ttt) REVERT: B 955 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7543 (ttt) REVERT: B 958 TYR cc_start: 0.7841 (m-10) cc_final: 0.6708 (m-80) REVERT: B 961 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7850 (tm-30) outliers start: 15 outliers final: 10 residues processed: 47 average time/residue: 0.0689 time to fit residues: 4.1296 Evaluate side-chains 45 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 902 ILE Chi-restraints excluded: chain B residue 955 MET Chi-restraints excluded: chain B residue 961 GLN Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 985 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 30 optimal weight: 9.9990 chunk 18 optimal weight: 0.0980 chunk 31 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.105249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080748 restraints weight = 9920.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083192 restraints weight = 4486.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084810 restraints weight = 2911.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085581 restraints weight = 2304.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086127 restraints weight = 2062.773| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4297 Z= 0.140 Angle : 0.924 8.063 6252 Z= 0.374 Chirality : 0.069 0.474 782 Planarity : 0.003 0.035 435 Dihedral : 18.774 159.860 1415 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 5.94 % Allowed : 31.05 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.57), residues: 236 helix: 2.11 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -0.85 (1.04), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 820 TYR 0.008 0.002 TYR B 815 PHE 0.007 0.001 PHE B 839 TRP 0.002 0.001 TRP B 990 HIS 0.000 0.000 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 4297) covalent geometry : angle 0.92392 / 0.37 ( 6252) hydrogen bonds : bond 0.06526 / 4.85 ( 233) hydrogen bonds : angle 2.94951 / 2.10 ( 563) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: B 762 ARG cc_start: 0.7950 (mmt90) cc_final: 0.6960 (tpt170) REVERT: B 775 MET cc_start: 0.6249 (tpt) cc_final: 0.5962 (ttt) REVERT: B 912 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 958 TYR cc_start: 0.7674 (m-10) cc_final: 0.6477 (m-10) REVERT: B 961 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7751 (tm-30) outliers start: 13 outliers final: 7 residues processed: 48 average time/residue: 0.0519 time to fit residues: 3.2085 Evaluate side-chains 40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 955 MET Chi-restraints excluded: chain B residue 961 GLN Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 810 ASN B 961 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075842 restraints weight = 10008.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078277 restraints weight = 4696.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079795 restraints weight = 3137.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.080644 restraints weight = 2547.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080657 restraints weight = 2277.090| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4297 Z= 0.254 Angle : 1.063 8.252 6252 Z= 0.432 Chirality : 0.077 0.512 782 Planarity : 0.004 0.028 435 Dihedral : 18.780 156.706 1415 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.48 % Allowed : 31.51 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.56), residues: 236 helix: 1.96 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -0.83 (1.03), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 820 TYR 0.006 0.002 TYR B 815 PHE 0.009 0.001 PHE B 959 TRP 0.009 0.003 TRP B 990 HIS 0.001 0.001 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 ( 4297) covalent geometry : angle 1.06343 / 0.43 ( 6252) hydrogen bonds : bond 0.06894 / 5.22 ( 233) hydrogen bonds : angle 3.25271 / 2.30 ( 563) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6486 (tpt) cc_final: 0.6033 (ttt) REVERT: B 955 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7588 (ttt) REVERT: B 958 TYR cc_start: 0.7824 (m-10) cc_final: 0.6752 (m-80) outliers start: 12 outliers final: 8 residues processed: 39 average time/residue: 0.0259 time to fit residues: 1.5128 Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 955 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 0.0370 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078664 restraints weight = 10112.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.081137 restraints weight = 4546.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.082746 restraints weight = 2952.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083495 restraints weight = 2340.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083782 restraints weight = 2098.927| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4297 Z= 0.170 Angle : 0.954 8.823 6252 Z= 0.387 Chirality : 0.071 0.491 782 Planarity : 0.003 0.028 435 Dihedral : 18.607 155.259 1415 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.48 % Allowed : 31.05 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.56), residues: 236 helix: 2.08 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.55 (1.04), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 820 TYR 0.006 0.001 TYR B 815 PHE 0.006 0.001 PHE B 959 TRP 0.006 0.002 TRP B 990 HIS 0.002 0.001 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 4297) covalent geometry : angle 0.95417 / 0.39 ( 6252) hydrogen bonds : bond 0.06447 / 4.84 ( 233) hydrogen bonds : angle 3.02821 / 2.13 ( 563) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6381 (tpt) cc_final: 0.6009 (ttt) REVERT: B 785 GLN cc_start: 0.8097 (mp10) cc_final: 0.7889 (mp10) REVERT: B 955 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7422 (ttt) REVERT: B 958 TYR cc_start: 0.7817 (m-10) cc_final: 0.6559 (m-10) outliers start: 12 outliers final: 9 residues processed: 44 average time/residue: 0.0447 time to fit residues: 2.6789 Evaluate side-chains 37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 955 MET Chi-restraints excluded: chain B residue 965 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.104273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078839 restraints weight = 10090.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081360 restraints weight = 4555.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082990 restraints weight = 2944.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083867 restraints weight = 2334.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084072 restraints weight = 2068.559| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4297 Z= 0.163 Angle : 0.949 9.810 6252 Z= 0.385 Chirality : 0.070 0.479 782 Planarity : 0.003 0.026 435 Dihedral : 18.539 155.262 1415 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 7.31 % Allowed : 31.05 % Favored : 61.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.56), residues: 236 helix: 2.18 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.67 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 877 TYR 0.006 0.001 TYR B 815 PHE 0.006 0.001 PHE B 959 TRP 0.005 0.002 TRP B 990 HIS 0.003 0.001 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 4297) covalent geometry : angle 0.94857 / 0.38 ( 6252) hydrogen bonds : bond 0.06351 / 4.80 ( 233) hydrogen bonds : angle 2.97384 / 2.09 ( 563) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6477 (tpt) cc_final: 0.6062 (ttt) REVERT: B 791 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: B 955 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7451 (ttt) REVERT: B 958 TYR cc_start: 0.7801 (m-10) cc_final: 0.6520 (m-10) outliers start: 16 outliers final: 11 residues processed: 46 average time/residue: 0.0400 time to fit residues: 2.7205 Evaluate side-chains 39 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 955 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 5 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 785 GLN B 810 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.100518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074198 restraints weight = 9998.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076603 restraints weight = 4638.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078187 restraints weight = 3091.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079055 restraints weight = 2476.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.079340 restraints weight = 2209.008| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4297 Z= 0.322 Angle : 1.161 10.273 6252 Z= 0.475 Chirality : 0.083 0.590 782 Planarity : 0.005 0.045 435 Dihedral : 18.904 156.761 1415 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 6.85 % Allowed : 31.51 % Favored : 61.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.55), residues: 236 helix: 1.62 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -1.55 (0.92), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 877 TYR 0.006 0.002 TYR B 815 PHE 0.012 0.002 PHE B 959 TRP 0.013 0.004 TRP B 990 HIS 0.006 0.003 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.32 ( 4297) covalent geometry : angle 1.16117 / 0.47 ( 6252) hydrogen bonds : bond 0.07531 / 5.67 ( 233) hydrogen bonds : angle 3.53936 / 2.49 ( 563) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.062 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6748 (tpt) cc_final: 0.6384 (ttt) REVERT: B 868 MET cc_start: 0.7480 (ttm) cc_final: 0.7105 (ttp) REVERT: B 955 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7672 (ttt) REVERT: B 958 TYR cc_start: 0.7906 (m-10) cc_final: 0.6858 (m-80) outliers start: 15 outliers final: 10 residues processed: 38 average time/residue: 0.0276 time to fit residues: 1.6159 Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 955 MET Chi-restraints excluded: chain B residue 965 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.106405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080869 restraints weight = 10062.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083396 restraints weight = 4508.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085084 restraints weight = 2892.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086074 restraints weight = 2271.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086475 restraints weight = 1985.687| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4297 Z= 0.136 Angle : 0.913 11.191 6252 Z= 0.370 Chirality : 0.068 0.442 782 Planarity : 0.003 0.028 435 Dihedral : 18.540 153.785 1415 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.48 % Allowed : 32.42 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.56), residues: 236 helix: 2.23 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -0.71 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 877 TYR 0.006 0.001 TYR B 815 PHE 0.018 0.002 PHE B 776 TRP 0.004 0.001 TRP B 990 HIS 0.002 0.001 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 4297) covalent geometry : angle 0.91256 / 0.37 ( 6252) hydrogen bonds : bond 0.06416 / 4.77 ( 233) hydrogen bonds : angle 2.90776 / 2.04 ( 563) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6588 (tpt) cc_final: 0.6270 (ttt) REVERT: B 791 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: B 899 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8459 (mm) REVERT: B 958 TYR cc_start: 0.7683 (m-10) cc_final: 0.7374 (m-10) outliers start: 12 outliers final: 6 residues processed: 37 average time/residue: 0.0506 time to fit residues: 2.6078 Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 927 HIS Chi-restraints excluded: chain B residue 965 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.108110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082485 restraints weight = 9907.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085079 restraints weight = 4498.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086713 restraints weight = 2896.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087565 restraints weight = 2289.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088050 restraints weight = 2036.551| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4297 Z= 0.126 Angle : 0.892 12.052 6252 Z= 0.362 Chirality : 0.067 0.429 782 Planarity : 0.003 0.032 435 Dihedral : 18.422 155.781 1415 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.20 % Allowed : 34.70 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.56), residues: 236 helix: 2.37 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -0.98 (1.02), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 820 TYR 0.006 0.001 TYR B 815 PHE 0.011 0.001 PHE B 839 TRP 0.002 0.001 TRP B 990 HIS 0.003 0.001 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 4297) covalent geometry : angle 0.89153 / 0.36 ( 6252) hydrogen bonds : bond 0.06038 / 4.57 ( 233) hydrogen bonds : angle 2.82836 / 1.99 ( 563) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6478 (tpt) cc_final: 0.5952 (ttt) REVERT: B 780 MET cc_start: 0.7023 (mmm) cc_final: 0.6423 (ttt) REVERT: B 791 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: B 958 TYR cc_start: 0.7585 (m-10) cc_final: 0.7357 (m-10) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.0427 time to fit residues: 2.1317 Evaluate side-chains 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 799 ASP Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 927 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.102483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076308 restraints weight = 10005.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078731 restraints weight = 4718.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080247 restraints weight = 3135.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.081127 restraints weight = 2519.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081454 restraints weight = 2241.563| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4297 Z= 0.268 Angle : 1.067 10.442 6252 Z= 0.436 Chirality : 0.076 0.522 782 Planarity : 0.005 0.050 435 Dihedral : 18.752 155.729 1413 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.74 % Allowed : 35.16 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.56), residues: 236 helix: 1.89 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -1.29 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 877 TYR 0.006 0.002 TYR B 815 PHE 0.012 0.002 PHE B 776 TRP 0.011 0.003 TRP B 990 HIS 0.005 0.002 HIS B 917 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.27 ( 4297) covalent geometry : angle 1.06735 / 0.44 ( 6252) hydrogen bonds : bond 0.06953 / 5.20 ( 233) hydrogen bonds : angle 3.32194 / 2.34 ( 563) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 757.75 seconds wall clock time: 13 minutes 47.90 seconds (827.90 seconds total)