Starting phenix.real_space_refine on Thu Mar 6 00:34:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7r_36046/03_2025/8j7r_36046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7r_36046/03_2025/8j7r_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7r_36046/03_2025/8j7r_36046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7r_36046/03_2025/8j7r_36046.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7r_36046/03_2025/8j7r_36046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7r_36046/03_2025/8j7r_36046.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'RNA': 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: 3.26, per 1000 atoms: 0.81 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: 1.16 Conformation dependent library (CDL) restraints added in 257.6 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: 1.66 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: 1.35 Time building geometry restraints manager: 1.33 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 - 1.39: 4586 1.39 - 2.78: 1355 2.78 - 4.17: 236 4.17 - 5.56: 67 5.56 - 6.95: 8 Bond angle restraints: 6252 Sorted by residual: angle pdb=" O3' U C 778 " pdb=" C3' U C 778 " pdb=" C2' U C 778 " ideal model delta sigma weight residual 113.70 120.65 -6.95 1.50e+00 4.44e-01 2.15e+01 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=" C4' U C 778 " pdb=" C3' U C 778 " pdb=" C2' U C 778 " ideal model delta sigma weight residual 102.60 98.18 4.42 1.00e+00 1.00e+00 1.96e+01 angle pdb=" C3' U C 778 " pdb=" C2' U C 778 " pdb=" O2' U C 778 " ideal model delta sigma weight residual 110.70 116.85 -6.15 1.50e+00 4.44e-01 1.68e+01 angle pdb=" C4' U C 685 " pdb=" C3' U C 685 " pdb=" O3' U C 685 " ideal model delta sigma weight residual 113.00 107.18 5.82 1.50e+00 4.44e-01 1.50e+01 ... (remaining 6247 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 31.70: 2371 31.70 - 63.39: 328 63.39 - 95.08: 69 95.08 - 126.77: 2 126.77 - 158.46: 1 Dihedral angle restraints: 2771 sinusoidal: 2070 harmonic: 701 Sorted by residual: dihedral pdb=" C5' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" O3' A C 687 " ideal model delta sinusoidal sigma weight residual 147.00 109.30 37.70 1 8.00e+00 1.56e-02 3.13e+01 dihedral pdb=" O4' A C 687 " pdb=" C4' A C 687 " pdb=" C3' A C 687 " pdb=" C2' A C 687 " ideal model delta sinusoidal sigma weight residual 24.00 -10.27 34.27 1 8.00e+00 1.56e-02 2.60e+01 dihedral pdb=" C3' A C 687 " pdb=" C4' A C 687 " pdb=" O4' A C 687 " pdb=" C1' A C 687 " ideal model delta sinusoidal sigma weight residual -2.00 29.65 -31.65 1 8.00e+00 1.56e-02 2.23e+01 ... (remaining 2768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 494 0.109 - 0.219: 206 0.219 - 0.328: 79 0.328 - 0.437: 0 0.437 - 0.546: 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 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.46e+00 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 2.41 2.93 -0.52 2.00e-01 2.50e+01 6.85e+00 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 2.41 2.93 -0.52 2.00e-01 2.50e+01 6.85e+00 ... (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: 0.150 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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= 0.591 Angle : 1.340 6.949 6252 Z= 0.867 Chirality : 0.128 0.546 782 Planarity : 0.005 0.026 435 Dihedral : 24.427 158.465 2309 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (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 TRP 0.009 0.003 TRP B 990 HIS 0.007 0.004 HIS B 917 PHE 0.032 0.005 PHE B 839 TYR 0.010 0.002 TYR B 815 ARG 0.008 0.001 ARG B 762 *********************** 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 : 0.321 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: 0.7363 (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: 0.7747 (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: 0.2298 time to fit residues: 23.3390 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 : 0.288 ------------------------------------------------------------------------------- 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 27 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.104316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078865 restraints weight = 9980.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081381 restraints weight = 4664.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083021 restraints weight = 3054.041| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4297 Z= 0.151 Angle : 0.574 7.615 6252 Z= 0.289 Chirality : 0.032 0.182 782 Planarity : 0.004 0.037 435 Dihedral : 23.644 167.504 1794 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 7.31 % Allowed : 25.57 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.55), residues: 236 helix: 1.67 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -1.01 (1.03), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 990 HIS 0.002 0.001 HIS B 917 PHE 0.013 0.002 PHE B 776 TYR 0.009 0.002 TYR B 815 ARG 0.004 0.000 ARG B 877 *********************** 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 67 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 775 MET cc_start: 0.6327 (tpt) cc_final: 0.5861 (ttt) REVERT: B 958 TYR cc_start: 0.7573 (m-10) cc_final: 0.6420 (m-10) REVERT: B 961 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7642 (tm-30) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.1824 time to fit residues: 13.6808 Evaluate side-chains 47 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 902 ILE 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 22 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 961 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.100941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074604 restraints weight = 9879.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076952 restraints weight = 4816.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.078449 restraints weight = 3267.656| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4297 Z= 0.246 Angle : 0.632 9.610 6252 Z= 0.311 Chirality : 0.034 0.229 782 Planarity : 0.004 0.033 435 Dihedral : 23.275 164.782 1779 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 6.39 % Allowed : 30.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.56), residues: 236 helix: 1.79 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -1.15 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 990 HIS 0.002 0.001 HIS B 917 PHE 0.023 0.002 PHE B 959 TYR 0.004 0.002 TYR B 815 ARG 0.003 0.001 ARG B 820 *********************** 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 53 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 775 MET cc_start: 0.6601 (tpt) cc_final: 0.6037 (ttt) REVERT: B 819 CYS cc_start: 0.8337 (m) cc_final: 0.7965 (m) REVERT: B 958 TYR cc_start: 0.7790 (m-10) cc_final: 0.6647 (m-10) outliers start: 14 outliers final: 11 residues processed: 48 average time/residue: 0.1675 time to fit residues: 10.0358 Evaluate side-chains 44 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 902 ILE Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076841 restraints weight = 9959.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079300 restraints weight = 4796.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.080861 restraints weight = 3192.545| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4297 Z= 0.157 Angle : 0.540 7.526 6252 Z= 0.265 Chirality : 0.030 0.192 782 Planarity : 0.003 0.028 435 Dihedral : 22.945 164.056 1777 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.02 % Allowed : 32.42 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.56), residues: 236 helix: 2.20 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.84 (1.07), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 990 HIS 0.002 0.001 HIS B 917 PHE 0.018 0.001 PHE B 959 TYR 0.008 0.002 TYR B 815 ARG 0.001 0.000 ARG B 820 *********************** 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 52 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 775 MET cc_start: 0.6362 (tpt) cc_final: 0.5886 (ttt) REVERT: B 791 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: B 818 MET cc_start: 0.8518 (tmm) cc_final: 0.8252 (ttt) REVERT: B 958 TYR cc_start: 0.7764 (m-10) cc_final: 0.6563 (m-10) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1321 time to fit residues: 8.2004 Evaluate side-chains 40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 800 LEU 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 965 ILE Chi-restraints excluded: chain B residue 971 THR 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 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 0.0270 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.103459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077359 restraints weight = 10307.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079850 restraints weight = 4961.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081493 restraints weight = 3294.142| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4297 Z= 0.140 Angle : 0.517 8.386 6252 Z= 0.252 Chirality : 0.029 0.187 782 Planarity : 0.003 0.028 435 Dihedral : 22.762 163.654 1773 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.02 % Allowed : 31.05 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.56), residues: 236 helix: 2.64 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -0.95 (1.00), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 990 HIS 0.001 0.001 HIS B 917 PHE 0.011 0.001 PHE B 959 TYR 0.007 0.002 TYR B 815 ARG 0.003 0.000 ARG B 877 *********************** 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 50 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6217 (tpt) cc_final: 0.5807 (ttt) REVERT: B 791 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: B 818 MET cc_start: 0.8509 (tmm) cc_final: 0.8266 (ttt) REVERT: B 819 CYS cc_start: 0.8392 (m) cc_final: 0.8090 (m) REVERT: B 863 LYS cc_start: 0.7030 (tmmt) cc_final: 0.6709 (tptp) REVERT: B 958 TYR cc_start: 0.7722 (m-10) cc_final: 0.6509 (m-10) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 0.1302 time to fit residues: 7.5637 Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.073601 restraints weight = 9812.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.075962 restraints weight = 4746.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077422 restraints weight = 3191.938| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4297 Z= 0.212 Angle : 0.576 8.873 6252 Z= 0.282 Chirality : 0.031 0.209 782 Planarity : 0.003 0.026 435 Dihedral : 22.795 162.746 1773 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 6.39 % Allowed : 32.88 % Favored : 60.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.55), residues: 236 helix: 2.45 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -1.41 (0.93), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 990 HIS 0.003 0.001 HIS B 917 PHE 0.007 0.001 PHE B 959 TYR 0.008 0.002 TYR B 815 ARG 0.002 0.000 ARG B 820 *********************** 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 46 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 775 MET cc_start: 0.6582 (tpt) cc_final: 0.6122 (ttt) REVERT: B 819 CYS cc_start: 0.8333 (m) cc_final: 0.8029 (m) REVERT: B 863 LYS cc_start: 0.7140 (tmmt) cc_final: 0.6785 (tptp) REVERT: B 899 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8738 (mm) REVERT: B 958 TYR cc_start: 0.7803 (m-10) cc_final: 0.6688 (m-10) outliers start: 14 outliers final: 9 residues processed: 44 average time/residue: 0.1667 time to fit residues: 9.1737 Evaluate side-chains 40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 927 HIS Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.102711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076573 restraints weight = 10051.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079098 restraints weight = 4681.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080732 restraints weight = 3072.440| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4297 Z= 0.135 Angle : 0.513 9.583 6252 Z= 0.253 Chirality : 0.029 0.187 782 Planarity : 0.003 0.027 435 Dihedral : 22.624 162.620 1773 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.11 % Allowed : 33.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.56), residues: 236 helix: 2.63 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -1.25 (0.95), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 990 HIS 0.001 0.001 HIS B 917 PHE 0.010 0.001 PHE B 959 TYR 0.008 0.002 TYR B 815 ARG 0.005 0.000 ARG B 877 *********************** 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 40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6674 (tpt) cc_final: 0.6147 (ttt) REVERT: B 791 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: B 819 CYS cc_start: 0.8362 (m) cc_final: 0.7923 (m) REVERT: B 863 LYS cc_start: 0.7295 (tmmt) cc_final: 0.6992 (tptp) REVERT: B 899 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8401 (mm) REVERT: B 958 TYR cc_start: 0.7643 (m-10) cc_final: 0.7357 (m-10) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.1351 time to fit residues: 6.8092 Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 982 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074854 restraints weight = 9867.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077263 restraints weight = 4787.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.078838 restraints weight = 3202.644| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4297 Z= 0.186 Angle : 0.553 10.354 6252 Z= 0.270 Chirality : 0.031 0.202 782 Planarity : 0.003 0.026 435 Dihedral : 22.651 162.333 1773 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.65 % Allowed : 33.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.56), residues: 236 helix: 2.56 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -1.19 (0.95), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 990 HIS 0.003 0.001 HIS B 917 PHE 0.008 0.001 PHE B 959 TYR 0.006 0.002 TYR B 815 ARG 0.005 0.000 ARG B 877 *********************** 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 43 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6586 (tpt) cc_final: 0.6211 (ttt) REVERT: B 791 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: B 819 CYS cc_start: 0.8241 (m) cc_final: 0.7935 (m) REVERT: B 863 LYS cc_start: 0.7323 (tmmt) cc_final: 0.7018 (tptp) REVERT: B 958 TYR cc_start: 0.7779 (m-10) cc_final: 0.7500 (m-10) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.1139 time to fit residues: 6.4470 Evaluate side-chains 38 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 982 VAL Chi-restraints excluded: chain B residue 985 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.102046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075874 restraints weight = 10081.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078353 restraints weight = 4814.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.079877 restraints weight = 3203.769| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4297 Z= 0.157 Angle : 0.531 10.721 6252 Z= 0.261 Chirality : 0.030 0.195 782 Planarity : 0.003 0.026 435 Dihedral : 22.573 162.450 1773 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.57 % Allowed : 33.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.56), residues: 236 helix: 2.53 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -1.12 (0.97), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 990 HIS 0.003 0.001 HIS B 917 PHE 0.014 0.001 PHE B 776 TYR 0.005 0.001 TYR B 815 ARG 0.004 0.000 ARG B 877 *********************** 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: 10 poor density : 30 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: B 775 MET cc_start: 0.6630 (tpt) cc_final: 0.6155 (ttt) REVERT: B 791 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: B 819 CYS cc_start: 0.8276 (m) cc_final: 0.7945 (m) REVERT: B 863 LYS cc_start: 0.7286 (tmmt) cc_final: 0.7010 (tptp) REVERT: B 899 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8546 (mm) REVERT: B 958 TYR cc_start: 0.7724 (m-10) cc_final: 0.7511 (m-10) outliers start: 10 outliers final: 6 residues processed: 38 average time/residue: 0.1101 time to fit residues: 5.8120 Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 965 ILE Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.102148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075944 restraints weight = 10045.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078403 restraints weight = 4772.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079936 restraints weight = 3168.936| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4297 Z= 0.159 Angle : 0.533 9.588 6252 Z= 0.265 Chirality : 0.030 0.195 782 Planarity : 0.003 0.024 435 Dihedral : 22.554 162.192 1773 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.56), residues: 236 helix: 2.52 (0.38), residues: 197 sheet: None (None), residues: 0 loop : -1.15 (0.97), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 990 HIS 0.002 0.001 HIS B 917 PHE 0.009 0.001 PHE B 776 TYR 0.005 0.001 TYR B 815 ARG 0.004 0.000 ARG B 877 ********************** 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 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 791 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: B 819 CYS cc_start: 0.8199 (m) cc_final: 0.7881 (m) REVERT: B 863 LYS cc_start: 0.7292 (tmmt) cc_final: 0.7009 (tptp) REVERT: B 899 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8565 (mm) REVERT: B 958 TYR cc_start: 0.7725 (m-10) cc_final: 0.7515 (m-10) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 0.1472 time to fit residues: 6.4703 Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 829 THR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.4980 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075127 restraints weight = 10031.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077502 restraints weight = 4855.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079037 restraints weight = 3256.344| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4297 Z= 0.203 Angle : 0.564 9.639 6252 Z= 0.280 Chirality : 0.031 0.207 782 Planarity : 0.003 0.025 435 Dihedral : 22.634 162.276 1772 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.20 % Allowed : 34.25 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.56), residues: 236 helix: 2.40 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -1.15 (0.98), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 990 HIS 0.004 0.001 HIS B 917 PHE 0.007 0.001 PHE B 959 TYR 0.004 0.002 TYR B 815 ARG 0.003 0.000 ARG B 877 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1369.20 seconds wall clock time: 24 minutes 54.65 seconds (1494.65 seconds total)