Starting phenix.real_space_refine on Thu Nov 14 20:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/11_2024/8huj_35041.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/11_2024/8huj_35041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/11_2024/8huj_35041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/11_2024/8huj_35041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/11_2024/8huj_35041.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8huj_35041/11_2024/8huj_35041.cif" } resolution = 3.76 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 99 5.49 5 Mg 3 5.21 5 S 35 5.16 5 C 4108 2.51 5 N 1261 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7143 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 372} 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: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2121 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 41} Link IDs: {'rna2p': 14, 'rna3p': 84} 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: 4.89, per 1000 atoms: 0.68 Number of scatterers: 7143 At special positions: 0 Unit cell: (100.98, 94.095, 119.34, 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 35 16.00 P 99 15.00 Mg 3 11.99 O 1637 8.00 N 1261 7.00 C 4108 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: 2.09 Conformation dependent library (CDL) restraints added in 790.8 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1186 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 65.1% alpha, 6.9% beta 37 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 4.101A pdb=" N ASN A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.564A pdb=" N GLY A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.207A pdb=" N PHE A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 139 through 150 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.585A pdb=" N LYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 257 through 269 removed outlier: 4.416A pdb=" N ASP A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.570A pdb=" N ASP A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.926A pdb=" N HIS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 removed outlier: 3.555A pdb=" N ARG A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.310A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 771 Processing helix chain 'B' and resid 775 through 785 removed outlier: 3.714A pdb=" N LEU B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 781 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 4.731A 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: 3.574A 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: 3.807A pdb=" N ASP B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU B 859 " --> pdb=" O LYS B 855 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU B 867 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 908 removed outlier: 3.609A pdb=" N LEU B 908 " --> pdb=" O GLU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 926 removed outlier: 3.591A pdb=" N MET B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 921 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 922 " --> pdb=" O ASP B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 947 removed outlier: 5.967A pdb=" N LYS B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 6.198A 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: 3.570A pdb=" N PHE B 959 " --> pdb=" O MET B 955 " (cutoff:3.500A) removed outlier: 3.954A 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 'A' and resid 131 through 133 removed outlier: 6.462A pdb=" N HIS A 132 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 104 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP A 182 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 106 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 179 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 212 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 181 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 72 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SER A 213 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 74 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 removed outlier: 6.490A pdb=" N SER A 300 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 275 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 328 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 277 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 827 through 828 269 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1756 1.33 - 1.46: 1895 1.46 - 1.58: 3551 1.58 - 1.70: 195 1.70 - 1.82: 60 Bond restraints: 7457 Sorted by residual: bond pdb=" N VAL B 835 " pdb=" CA VAL B 835 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.32e-02 5.74e+03 8.07e+00 bond pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N MET A 187 " pdb=" CA MET A 187 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N LYS A 369 " pdb=" CA LYS A 369 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.19e-02 7.06e+03 6.73e+00 bond pdb=" N VAL A 180 " pdb=" CA VAL A 180 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.41e+00 ... (remaining 7452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10096 1.97 - 3.93: 369 3.93 - 5.90: 52 5.90 - 7.87: 9 7.87 - 9.83: 1 Bond angle restraints: 10527 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 113.80 119.00 -5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" O3' U C 778 " pdb=" C3' U C 778 " pdb=" C2' U C 778 " ideal model delta sigma weight residual 113.70 121.48 -7.78 1.50e+00 4.44e-01 2.69e+01 angle pdb=" N ARG A 368 " pdb=" CA ARG A 368 " pdb=" C ARG A 368 " ideal model delta sigma weight residual 111.28 106.15 5.13 1.09e+00 8.42e-01 2.22e+01 angle pdb=" C4' U C 778 " pdb=" C3' U C 778 " pdb=" O3' U C 778 " ideal model delta sigma weight residual 113.00 119.98 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" CA VAL B 835 " pdb=" C VAL B 835 " pdb=" O VAL B 835 " ideal model delta sigma weight residual 121.92 117.02 4.90 1.17e+00 7.31e-01 1.75e+01 ... (remaining 10522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 4196 31.18 - 62.37: 405 62.37 - 93.55: 108 93.55 - 124.74: 2 124.74 - 155.92: 1 Dihedral angle restraints: 4712 sinusoidal: 2893 harmonic: 1819 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 147.00 108.10 38.90 1 8.00e+00 1.56e-02 3.33e+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 -8.41 32.41 1 8.00e+00 1.56e-02 2.34e+01 dihedral pdb=" O4' A C 687 " pdb=" C1' A C 687 " pdb=" N9 A C 687 " pdb=" C4 A C 687 " ideal model delta sinusoidal sigma weight residual -106.00 -172.85 66.85 1 1.70e+01 3.46e-03 2.02e+01 ... (remaining 4709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1157 0.101 - 0.202: 94 0.202 - 0.302: 22 0.302 - 0.403: 1 0.403 - 0.504: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" C3' U C 778 " pdb=" C4' U C 778 " pdb=" O3' U C 778 " pdb=" C2' U C 778 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" C3' A C 771 " pdb=" C4' A C 771 " pdb=" O3' A C 771 " pdb=" C2' A C 771 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" P G C 766 " pdb=" OP1 G C 766 " pdb=" OP2 G C 766 " pdb=" O5' G C 766 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1272 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 158 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.48e+00 pdb=" C THR A 158 " 0.047 2.00e-02 2.50e+03 pdb=" O THR A 158 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 64 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 65 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 86 " 0.013 2.00e-02 2.50e+03 1.39e-02 3.37e+00 pdb=" CG PHE A 86 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 86 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 86 " 0.002 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 829 2.74 - 3.28: 7178 3.28 - 3.82: 13651 3.82 - 4.36: 15716 4.36 - 4.90: 22689 Nonbonded interactions: 60063 Sorted by model distance: nonbonded pdb=" O ASP A 348 " pdb=" NH1 ARG A 359 " model vdw 2.203 3.120 nonbonded pdb=" O CYS B 936 " pdb=" OG1 THR B 940 " model vdw 2.209 3.040 nonbonded pdb=" O ILE A 246 " pdb=" NE2 GLN A 248 " model vdw 2.244 3.120 nonbonded pdb=" O2 C C 746 " pdb=" N6 A C 750 " model vdw 2.249 3.120 nonbonded pdb=" N GLU A 379 " pdb=" OE1 GLU A 379 " model vdw 2.278 3.120 ... (remaining 60058 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: 0.090 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.900 Find NCS groups from input model: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.005 0.038 7457 Z= 0.314 Angle : 0.828 9.832 10527 Z= 0.518 Chirality : 0.062 0.504 1275 Planarity : 0.004 0.048 979 Dihedral : 22.476 155.919 3526 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.51 % Allowed : 26.21 % Favored : 71.27 % 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: -0.39 (0.34), residues: 617 helix: 0.44 (0.28), residues: 340 sheet: -0.76 (0.64), residues: 61 loop : -1.08 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 287 HIS 0.003 0.001 HIS A 303 PHE 0.032 0.003 PHE A 86 TYR 0.009 0.002 TYR A 170 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.5083 (mtm) cc_final: 0.4264 (mtm) REVERT: A 228 MET cc_start: 0.4751 (tmm) cc_final: 0.4451 (tmm) REVERT: B 845 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7996 (t0) REVERT: B 890 ILE cc_start: 0.8839 (mm) cc_final: 0.8495 (mm) outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 0.2322 time to fit residues: 22.7849 Evaluate side-chains 66 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 845 ASN Chi-restraints excluded: chain B residue 893 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 0.0070 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 overall best weight: 5.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7457 Z= 0.301 Angle : 0.688 14.461 10527 Z= 0.346 Chirality : 0.039 0.227 1275 Planarity : 0.004 0.042 979 Dihedral : 21.928 164.363 2234 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.95 % Allowed : 26.75 % Favored : 69.30 % 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: 0.01 (0.35), residues: 617 helix: 0.63 (0.27), residues: 362 sheet: -0.88 (0.60), residues: 68 loop : -0.66 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 287 HIS 0.003 0.001 HIS B 927 PHE 0.040 0.003 PHE B 977 TYR 0.017 0.002 TYR A 48 ARG 0.006 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.6336 (tmm) cc_final: 0.5877 (ppp) REVERT: A 228 MET cc_start: 0.4762 (tmm) cc_final: 0.4387 (tmm) REVERT: A 293 HIS cc_start: 0.7869 (t-90) cc_final: 0.7621 (t-90) REVERT: B 853 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6890 (ptpt) REVERT: B 890 ILE cc_start: 0.8789 (mm) cc_final: 0.8483 (mm) REVERT: B 961 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8514 (tp-100) outliers start: 22 outliers final: 13 residues processed: 84 average time/residue: 0.2095 time to fit residues: 23.4699 Evaluate side-chains 77 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 798 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 853 LYS 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 961 GLN Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 982 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.0470 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7457 Z= 0.140 Angle : 0.538 14.088 10527 Z= 0.268 Chirality : 0.036 0.182 1275 Planarity : 0.003 0.040 979 Dihedral : 21.261 163.098 2226 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.95 % Allowed : 25.85 % Favored : 70.20 % 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: 0.47 (0.35), residues: 617 helix: 1.25 (0.28), residues: 362 sheet: -1.04 (0.60), residues: 68 loop : -0.91 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 287 HIS 0.003 0.001 HIS A 132 PHE 0.033 0.002 PHE B 977 TYR 0.009 0.001 TYR A 197 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.2086 (ptt) cc_final: 0.1101 (mtm) REVERT: A 161 ARG cc_start: 0.7549 (mtt-85) cc_final: 0.7318 (mtp85) REVERT: A 178 MET cc_start: 0.5161 (mtm) cc_final: 0.4922 (mtm) REVERT: A 187 MET cc_start: 0.6537 (tmm) cc_final: 0.6141 (ppp) REVERT: A 193 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.4698 (tptt) REVERT: A 228 MET cc_start: 0.4723 (tmm) cc_final: 0.4453 (tmm) REVERT: A 229 ARG cc_start: 0.6106 (ptp-170) cc_final: 0.5563 (mmp-170) REVERT: A 293 HIS cc_start: 0.7822 (t-90) cc_final: 0.7593 (t-90) REVERT: A 366 PHE cc_start: 0.3332 (OUTLIER) cc_final: 0.3019 (p90) REVERT: B 853 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6850 (ptpt) REVERT: B 855 LYS cc_start: 0.7242 (mmtm) cc_final: 0.6768 (mttm) REVERT: B 890 ILE cc_start: 0.8740 (mm) cc_final: 0.8430 (mm) REVERT: B 893 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8165 (ttm-80) REVERT: B 986 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6945 (ttt-90) outliers start: 22 outliers final: 8 residues processed: 96 average time/residue: 0.2545 time to fit residues: 31.2598 Evaluate side-chains 77 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 893 ARG Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 40.0000 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 960 ASN B 961 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7457 Z= 0.157 Angle : 0.541 16.330 10527 Z= 0.268 Chirality : 0.035 0.187 1275 Planarity : 0.003 0.038 979 Dihedral : 21.105 162.490 2225 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.49 % Allowed : 26.21 % Favored : 69.30 % 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: 0.78 (0.35), residues: 617 helix: 1.49 (0.28), residues: 358 sheet: -0.82 (0.65), residues: 60 loop : -0.77 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 27 HIS 0.002 0.001 HIS A 303 PHE 0.026 0.002 PHE B 977 TYR 0.009 0.001 TYR A 48 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.2003 (ptt) cc_final: 0.0884 (mtm) REVERT: A 178 MET cc_start: 0.5115 (mtm) cc_final: 0.4861 (mtm) REVERT: A 187 MET cc_start: 0.6610 (tmm) cc_final: 0.6256 (ppp) REVERT: A 229 ARG cc_start: 0.6178 (ptp-170) cc_final: 0.5325 (mmp-170) REVERT: A 293 HIS cc_start: 0.7804 (t-90) cc_final: 0.7515 (t70) REVERT: A 366 PHE cc_start: 0.3507 (OUTLIER) cc_final: 0.3296 (p90) REVERT: B 791 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: B 855 LYS cc_start: 0.7327 (mmtm) cc_final: 0.6887 (mttm) REVERT: B 986 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7049 (ttt-90) outliers start: 25 outliers final: 14 residues processed: 86 average time/residue: 0.2262 time to fit residues: 25.5949 Evaluate side-chains 81 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 857 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 50.0000 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7457 Z= 0.188 Angle : 0.560 16.104 10527 Z= 0.279 Chirality : 0.036 0.198 1275 Planarity : 0.004 0.037 979 Dihedral : 21.113 162.185 2221 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.21 % Allowed : 26.75 % Favored : 68.04 % 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: 0.78 (0.35), residues: 617 helix: 1.52 (0.28), residues: 359 sheet: -0.81 (0.62), residues: 68 loop : -0.83 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 27 HIS 0.002 0.001 HIS A 303 PHE 0.026 0.002 PHE B 977 TYR 0.010 0.001 TYR A 48 ARG 0.007 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.1945 (ptt) cc_final: 0.0770 (mtm) REVERT: A 178 MET cc_start: 0.5187 (mtm) cc_final: 0.4920 (mtm) REVERT: A 187 MET cc_start: 0.6491 (tmm) cc_final: 0.6163 (ppp) REVERT: A 366 PHE cc_start: 0.3375 (OUTLIER) cc_final: 0.3170 (p90) REVERT: B 791 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: B 853 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6809 (ptpt) REVERT: B 855 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6833 (mttm) REVERT: B 986 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7023 (ttt-90) outliers start: 29 outliers final: 18 residues processed: 89 average time/residue: 0.2142 time to fit residues: 25.3728 Evaluate side-chains 86 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7457 Z= 0.255 Angle : 0.626 16.722 10527 Z= 0.312 Chirality : 0.038 0.215 1275 Planarity : 0.004 0.037 979 Dihedral : 21.297 162.525 2221 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.03 % Allowed : 27.65 % Favored : 67.32 % 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: 0.62 (0.35), residues: 617 helix: 1.34 (0.27), residues: 358 sheet: -0.84 (0.62), residues: 68 loop : -0.77 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 258 HIS 0.003 0.001 HIS B 917 PHE 0.025 0.002 PHE B 977 TYR 0.013 0.002 TYR A 48 ARG 0.005 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.5308 (mtm) cc_final: 0.4994 (mtm) REVERT: B 791 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: B 855 LYS cc_start: 0.7032 (mmtm) cc_final: 0.6698 (mttm) REVERT: B 977 PHE cc_start: 0.7911 (m-10) cc_final: 0.7673 (m-80) REVERT: B 986 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7032 (ttt-90) outliers start: 28 outliers final: 21 residues processed: 87 average time/residue: 0.2152 time to fit residues: 24.7755 Evaluate side-chains 85 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7457 Z= 0.166 Angle : 0.567 16.341 10527 Z= 0.279 Chirality : 0.036 0.189 1275 Planarity : 0.003 0.038 979 Dihedral : 21.052 162.845 2221 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.67 % Allowed : 28.01 % Favored : 67.32 % 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: 0.74 (0.35), residues: 617 helix: 1.52 (0.28), residues: 359 sheet: -0.87 (0.69), residues: 55 loop : -0.92 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 287 HIS 0.002 0.001 HIS A 303 PHE 0.020 0.002 PHE B 776 TYR 0.008 0.001 TYR A 267 ARG 0.004 0.000 ARG B 877 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.1863 (ptt) cc_final: 0.0692 (mtm) REVERT: A 178 MET cc_start: 0.5472 (mtm) cc_final: 0.5264 (mtm) REVERT: A 258 TRP cc_start: 0.8325 (m-10) cc_final: 0.8016 (m-10) REVERT: A 366 PHE cc_start: 0.3476 (OUTLIER) cc_final: 0.3246 (p90) REVERT: B 791 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: B 855 LYS cc_start: 0.7045 (mmtm) cc_final: 0.6721 (mttm) REVERT: B 977 PHE cc_start: 0.7810 (m-10) cc_final: 0.7568 (m-10) REVERT: B 986 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6990 (ttt-90) outliers start: 26 outliers final: 21 residues processed: 85 average time/residue: 0.2088 time to fit residues: 24.4563 Evaluate side-chains 87 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL 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 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7457 Z= 0.155 Angle : 0.544 15.592 10527 Z= 0.269 Chirality : 0.035 0.182 1275 Planarity : 0.003 0.039 979 Dihedral : 20.887 162.827 2221 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.67 % Allowed : 27.83 % Favored : 67.50 % 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: 0.88 (0.35), residues: 617 helix: 1.64 (0.28), residues: 359 sheet: -0.49 (0.71), residues: 51 loop : -1.01 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS A 303 PHE 0.020 0.002 PHE B 977 TYR 0.011 0.001 TYR A 347 ARG 0.004 0.000 ARG B 877 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.7341 (m-80) cc_final: 0.7016 (m-80) REVERT: A 149 MET cc_start: 0.1740 (ptt) cc_final: 0.0622 (mtm) REVERT: A 178 MET cc_start: 0.5495 (mtm) cc_final: 0.5288 (mtm) REVERT: A 258 TRP cc_start: 0.8206 (m-10) cc_final: 0.7975 (m-10) REVERT: A 366 PHE cc_start: 0.3369 (OUTLIER) cc_final: 0.3097 (p90) REVERT: B 791 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: B 834 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8438 (m) REVERT: B 855 LYS cc_start: 0.7007 (mmtm) cc_final: 0.6653 (mttm) REVERT: B 977 PHE cc_start: 0.7803 (m-10) cc_final: 0.7566 (m-10) REVERT: B 986 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7043 (ttt-90) outliers start: 26 outliers final: 19 residues processed: 83 average time/residue: 0.1779 time to fit residues: 20.0956 Evaluate side-chains 86 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL 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 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 0.4980 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7457 Z= 0.258 Angle : 0.629 16.750 10527 Z= 0.311 Chirality : 0.038 0.224 1275 Planarity : 0.004 0.037 979 Dihedral : 21.144 162.824 2221 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.21 % Allowed : 27.29 % Favored : 67.50 % 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: 0.60 (0.35), residues: 617 helix: 1.36 (0.27), residues: 359 sheet: -0.80 (0.64), residues: 62 loop : -0.92 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 287 HIS 0.004 0.001 HIS B 927 PHE 0.020 0.002 PHE B 977 TYR 0.013 0.002 TYR A 48 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 143 GLU cc_start: 0.2581 (OUTLIER) cc_final: 0.2238 (mt-10) REVERT: A 149 MET cc_start: 0.1821 (ptt) cc_final: 0.0611 (mtm) REVERT: A 178 MET cc_start: 0.5721 (mtm) cc_final: 0.5395 (mtm) REVERT: A 258 TRP cc_start: 0.8334 (m-10) cc_final: 0.8097 (m-10) REVERT: A 366 PHE cc_start: 0.3537 (OUTLIER) cc_final: 0.3295 (p90) REVERT: B 776 PHE cc_start: 0.7835 (t80) cc_final: 0.7419 (t80) REVERT: B 791 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: B 855 LYS cc_start: 0.6987 (mmtm) cc_final: 0.6645 (mttm) REVERT: B 977 PHE cc_start: 0.7864 (m-10) cc_final: 0.7596 (m-10) REVERT: B 986 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7017 (ttt-90) outliers start: 29 outliers final: 22 residues processed: 83 average time/residue: 0.2220 time to fit residues: 24.5176 Evaluate side-chains 85 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL 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 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7457 Z= 0.272 Angle : 0.632 16.302 10527 Z= 0.315 Chirality : 0.038 0.216 1275 Planarity : 0.004 0.036 979 Dihedral : 21.223 163.213 2221 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.21 % Allowed : 27.47 % Favored : 67.32 % 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: 0.44 (0.35), residues: 617 helix: 1.19 (0.27), residues: 359 sheet: -0.70 (0.65), residues: 60 loop : -0.96 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 287 HIS 0.003 0.001 HIS B 927 PHE 0.022 0.002 PHE B 977 TYR 0.014 0.002 TYR A 267 ARG 0.004 0.000 ARG A 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.680 Fit side-chains REVERT: A 149 MET cc_start: 0.2093 (ptt) cc_final: 0.1003 (mtm) REVERT: A 366 PHE cc_start: 0.3516 (OUTLIER) cc_final: 0.3262 (p90) REVERT: B 776 PHE cc_start: 0.7865 (t80) cc_final: 0.7316 (t80) REVERT: B 791 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: B 855 LYS cc_start: 0.7026 (mmtm) cc_final: 0.6695 (mttm) REVERT: B 977 PHE cc_start: 0.7851 (m-10) cc_final: 0.7574 (m-10) REVERT: B 986 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7035 (ttt-90) outliers start: 29 outliers final: 25 residues processed: 86 average time/residue: 0.2055 time to fit residues: 23.7111 Evaluate side-chains 89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 982 VAL Chi-restraints excluded: chain B residue 986 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.102248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.069291 restraints weight = 21601.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.071463 restraints weight = 10692.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072541 restraints weight = 7562.068| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7457 Z= 0.281 Angle : 0.647 17.525 10527 Z= 0.321 Chirality : 0.039 0.219 1275 Planarity : 0.004 0.037 979 Dihedral : 21.254 163.425 2221 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.21 % Allowed : 27.83 % Favored : 66.97 % 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: 0.32 (0.34), residues: 617 helix: 1.06 (0.27), residues: 359 sheet: -0.52 (0.71), residues: 53 loop : -1.02 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 27 HIS 0.003 0.001 HIS B 927 PHE 0.020 0.002 PHE B 977 TYR 0.015 0.002 TYR A 267 ARG 0.004 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1346.55 seconds wall clock time: 33 minutes 14.45 seconds (1994.45 seconds total)