Starting phenix.real_space_refine on Fri Sep 11 03:39:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xw2_33489/09_2026/7xw2_33489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xw2_33489/09_2026/7xw2_33489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xw2_33489/09_2026/7xw2_33489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xw2_33489/09_2026/7xw2_33489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xw2_33489/09_2026/7xw2_33489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xw2_33489/09_2026/7xw2_33489.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xw2_33489/09_2026/7xw2_33489.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xw2_33489/09_2026/7xw2_33489.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 Ca 2 9.91 5 P 52 5.49 5 S 29 5.16 5 C 4279 2.51 5 N 1182 2.21 5 O 1448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6992 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5854 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 50, 'TRANS': 674} Chain breaks: 4 Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1136 Classifications: {'RNAv2': 54} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 27} Link IDs: {'rna2p': 2, 'rna3p': 51} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.54, per 1000 atoms: 0.22 Number of scatterers: 6992 At special positions: 0 Unit cell: (78.108, 83.202, 139.236, 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) Ca 2 19.99 S 29 16.00 P 52 15.00 O 1448 8.00 N 1182 7.00 C 4279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 278.4 milliseconds 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 44.0% alpha, 6.8% beta 10 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 754 through 758 Processing helix chain 'A' and resid 839 through 855 Processing helix chain 'A' and resid 968 through 976 removed outlier: 3.657A pdb=" N TYR A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 removed outlier: 4.079A pdb=" N ALA A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1053 removed outlier: 4.103A pdb=" N LYS A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1061 Processing helix chain 'A' and resid 1068 through 1074 Processing helix chain 'A' and resid 1293 through 1298 Processing helix chain 'A' and resid 1315 through 1335 removed outlier: 3.508A pdb=" N GLY A1319 " --> pdb=" O LEU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1352 through 1364 removed outlier: 3.781A pdb=" N LYS A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1369 removed outlier: 4.017A pdb=" N ARG A1368 " --> pdb=" O GLY A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1380 Processing helix chain 'A' and resid 1555 through 1575 removed outlier: 3.975A pdb=" N ILE A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A1564 " --> pdb=" O ALA A1560 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1567 " --> pdb=" O VAL A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1587 Processing helix chain 'A' and resid 1665 through 1674 removed outlier: 3.944A pdb=" N PHE A1669 " --> pdb=" O GLY A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1686 Processing helix chain 'A' and resid 1701 through 1722 removed outlier: 3.597A pdb=" N GLU A1705 " --> pdb=" O TYR A1701 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A1706 " --> pdb=" O GLN A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1741 Processing helix chain 'A' and resid 1741 through 1752 removed outlier: 3.629A pdb=" N TYR A1752 " --> pdb=" O LEU A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1758 removed outlier: 3.594A pdb=" N TYR A1757 " --> pdb=" O TYR A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1777 removed outlier: 3.866A pdb=" N VAL A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A1769 " --> pdb=" O LEU A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1812 removed outlier: 3.608A pdb=" N GLY A1809 " --> pdb=" O PRO A1805 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A1812 " --> pdb=" O MET A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1823 removed outlier: 3.753A pdb=" N GLY A1817 " --> pdb=" O GLU A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1849 removed outlier: 3.661A pdb=" N VAL A1830 " --> pdb=" O SER A1826 " (cutoff:3.500A) Proline residue: A1836 - end of helix Proline residue: A1840 - end of helix removed outlier: 4.615A pdb=" N ALA A1847 " --> pdb=" O GLU A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1861 Processing helix chain 'A' and resid 1896 through 1912 removed outlier: 3.817A pdb=" N SER A1911 " --> pdb=" O ARG A1907 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1912 " --> pdb=" O ALA A1908 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 747 through 750 Processing sheet with id=AA2, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AA3, first strand: chain 'A' and resid 801 through 804 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 820 removed outlier: 3.762A pdb=" N THR A 820 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 823 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.742A pdb=" N GLU A 866 " --> pdb=" O VAL A1386 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A1386 " --> pdb=" O GLU A 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1032 through 1033 removed outlier: 3.506A pdb=" N LEU A1033 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 930 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 931 " --> pdb=" O HIS A1041 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1871 through 1872 removed outlier: 3.638A pdb=" N GLU A1871 " --> pdb=" O ARG A1879 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1881 through 1883 210 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1028 1.31 - 1.44: 2237 1.44 - 1.56: 3854 1.56 - 1.69: 104 1.69 - 1.81: 42 Bond restraints: 7265 Sorted by residual: bond pdb=" N THR A 955 " pdb=" CA THR A 955 " ideal model delta sigma weight residual 1.455 1.489 -0.034 7.00e-03 2.04e+04 2.30e+01 bond pdb=" N ILE A 933 " pdb=" CA ILE A 933 " ideal model delta sigma weight residual 1.460 1.502 -0.042 9.30e-03 1.16e+04 2.00e+01 bond pdb=" N VAL A1804 " pdb=" CA VAL A1804 " ideal model delta sigma weight residual 1.461 1.499 -0.038 9.10e-03 1.21e+04 1.76e+01 bond pdb=" N LYS A 862 " pdb=" CA LYS A 862 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.54e+01 bond pdb=" N ILE A1802 " pdb=" CA ILE A1802 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.11e-02 8.12e+03 1.45e+01 ... (remaining 7260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 9513 2.34 - 4.68: 533 4.68 - 7.02: 43 7.02 - 9.35: 8 9.35 - 11.69: 3 Bond angle restraints: 10100 Sorted by residual: angle pdb=" N GLU A1068 " pdb=" CA GLU A1068 " pdb=" C GLU A1068 " ideal model delta sigma weight residual 112.93 101.24 11.69 1.12e+00 7.97e-01 1.09e+02 angle pdb=" N LEU A1065 " pdb=" CA LEU A1065 " pdb=" C LEU A1065 " ideal model delta sigma weight residual 111.28 101.22 10.06 1.09e+00 8.42e-01 8.51e+01 angle pdb=" N GLU A1069 " pdb=" CA GLU A1069 " pdb=" C GLU A1069 " ideal model delta sigma weight residual 112.38 105.22 7.16 1.22e+00 6.72e-01 3.44e+01 angle pdb=" N LEU A1315 " pdb=" CA LEU A1315 " pdb=" C LEU A1315 " ideal model delta sigma weight residual 114.56 107.21 7.35 1.27e+00 6.20e-01 3.35e+01 angle pdb=" N LEU A1061 " pdb=" CA LEU A1061 " pdb=" C LEU A1061 " ideal model delta sigma weight residual 111.71 105.23 6.48 1.15e+00 7.56e-01 3.18e+01 ... (remaining 10095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3856 17.65 - 35.31: 317 35.31 - 52.96: 89 52.96 - 70.61: 29 70.61 - 88.27: 15 Dihedral angle restraints: 4306 sinusoidal: 2154 harmonic: 2152 Sorted by residual: dihedral pdb=" C4' U C 24 " pdb=" C3' U C 24 " pdb=" C2' U C 24 " pdb=" C1' U C 24 " ideal model delta sinusoidal sigma weight residual 36.34 -35.94 72.29 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' U C 1 " pdb=" C3' U C 1 " pdb=" C2' U C 1 " pdb=" C1' U C 1 " ideal model delta sinusoidal sigma weight residual 36.34 -34.50 70.85 1 3.10e+00 1.04e-01 6.71e+02 dihedral pdb=" O4' U C 24 " pdb=" C4' U C 24 " pdb=" C3' U C 24 " pdb=" C2' U C 24 " ideal model delta sinusoidal sigma weight residual -35.15 23.24 -58.39 1 4.00e+00 6.25e-02 2.85e+02 ... (remaining 4303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 915 0.075 - 0.151: 148 0.151 - 0.226: 56 0.226 - 0.302: 49 0.302 - 0.377: 3 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA THR A1066 " pdb=" N THR A1066 " pdb=" C THR A1066 " pdb=" CB THR A1066 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA LEU A 890 " pdb=" N LEU A 890 " pdb=" C LEU A 890 " pdb=" CB LEU A 890 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASN A 938 " pdb=" N ASN A 938 " pdb=" C ASN A 938 " pdb=" CB ASN A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1168 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1332 " -0.018 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C PHE A1332 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE A1332 " -0.022 2.00e-02 2.50e+03 pdb=" N CYS A1333 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1063 " -0.016 2.00e-02 2.50e+03 3.38e-02 1.15e+01 pdb=" C CYS A1063 " 0.058 2.00e-02 2.50e+03 pdb=" O CYS A1063 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A1064 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1314 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ARG A1314 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG A1314 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A1315 " 0.019 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 18 2.49 - 3.09: 4796 3.09 - 3.70: 10579 3.70 - 4.30: 15726 4.30 - 4.90: 24783 Nonbonded interactions: 55902 Sorted by model distance: nonbonded pdb=" OE2 GLU A1705 " pdb="CA CA A2002 " model vdw 1.891 2.510 nonbonded pdb=" OP1 C C 52 " pdb="CA CA A2001 " model vdw 1.983 2.510 nonbonded pdb=" OP1 U C 23 " pdb="CA CA A2002 " model vdw 2.043 2.510 nonbonded pdb=" O2' U C 24 " pdb=" OP2 A C 25 " model vdw 2.385 3.040 nonbonded pdb=" O SER A 760 " pdb=" OG SER A 760 " model vdw 2.385 3.040 ... (remaining 55897 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 7265 Z= 0.473 Angle : 1.099 11.692 10100 Z= 0.719 Chirality : 0.085 0.377 1171 Planarity : 0.007 0.054 1092 Dihedral : 15.429 88.268 2914 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.92 % Allowed : 6.91 % Favored : 92.17 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.26), residues: 715 helix: -1.82 (0.27), residues: 284 sheet: -3.43 (0.51), residues: 49 loop : -2.32 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 906 TYR 0.025 0.003 TYR A1754 PHE 0.017 0.003 PHE A1745 TRP 0.031 0.004 TRP A1048 HIS 0.010 0.002 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.47 ( 7265) covalent geometry : angle 1.09939 / 0.72 (10100) hydrogen bonds : bond 0.20354 / 13.28 ( 233) hydrogen bonds : angle 8.03544 / 5.85 ( 634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.237 Fit side-chains REVERT: A 895 LYS cc_start: 0.8157 (mppt) cc_final: 0.7644 (ttpp) outliers start: 6 outliers final: 2 residues processed: 104 average time/residue: 0.0980 time to fit residues: 13.0727 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1705 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 928 GLN A 938 ASN A 985 GLN A1006 ASN A1029 ASN A1062 HIS A1073 GLN A1293 ASN A1379 ASN A1389 GLN A1689 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.203241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.162223 restraints weight = 8481.298| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.51 r_work: 0.3998 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7265 Z= 0.133 Angle : 0.729 11.515 10100 Z= 0.339 Chirality : 0.056 0.644 1171 Planarity : 0.005 0.047 1092 Dihedral : 11.428 77.852 1447 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.38 % Allowed : 11.98 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.28), residues: 715 helix: -0.51 (0.30), residues: 290 sheet: -2.94 (0.52), residues: 51 loop : -1.81 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1855 TYR 0.033 0.002 TYR A 946 PHE 0.025 0.002 PHE A 960 TRP 0.008 0.001 TRP A1048 HIS 0.019 0.002 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7265) covalent geometry : angle 0.72885 / 0.34 (10100) hydrogen bonds : bond 0.05065 / 3.45 ( 233) hydrogen bonds : angle 5.22240 / 3.89 ( 634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.163 Fit side-chains REVERT: A 844 GLU cc_start: 0.8252 (mp0) cc_final: 0.8022 (mp0) REVERT: A 856 HIS cc_start: 0.6864 (m90) cc_final: 0.6663 (t-90) REVERT: A 1357 TYR cc_start: 0.6787 (t80) cc_final: 0.6499 (t80) REVERT: A 1705 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5666 (pp20) REVERT: A 1808 MET cc_start: 0.6371 (mmp) cc_final: 0.6130 (mmp) REVERT: A 1859 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.6074 (mp0) outliers start: 9 outliers final: 4 residues processed: 75 average time/residue: 0.0650 time to fit residues: 6.9203 Evaluate side-chains 59 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1697 ILE Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 850 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.194815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.153675 restraints weight = 8504.116| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.37 r_work: 0.3890 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7265 Z= 0.228 Angle : 0.794 8.716 10100 Z= 0.374 Chirality : 0.057 0.674 1171 Planarity : 0.006 0.054 1092 Dihedral : 11.347 79.839 1447 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.46 % Allowed : 11.21 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.29), residues: 715 helix: -0.53 (0.29), residues: 289 sheet: -2.26 (0.56), residues: 68 loop : -1.91 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1855 TYR 0.029 0.002 TYR A 946 PHE 0.021 0.003 PHE A 960 TRP 0.009 0.002 TRP A1048 HIS 0.008 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 ( 7265) covalent geometry : angle 0.79425 / 0.37 (10100) hydrogen bonds : bond 0.06059 / 4.04 ( 233) hydrogen bonds : angle 5.36905 / 3.97 ( 634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.221 Fit side-chains REVERT: A 844 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: A 856 HIS cc_start: 0.7142 (m90) cc_final: 0.6716 (t70) REVERT: A 895 LYS cc_start: 0.8456 (mppt) cc_final: 0.7685 (ttpp) REVERT: A 1357 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6607 (t80) REVERT: A 1808 MET cc_start: 0.6419 (mmp) cc_final: 0.6077 (mmp) REVERT: A 1859 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6152 (mp0) outliers start: 16 outliers final: 8 residues processed: 66 average time/residue: 0.0902 time to fit residues: 7.8858 Evaluate side-chains 60 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1859 GLU Chi-restraints excluded: chain A residue 1881 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1549 HIS ** 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 = 0.4542 r_free = 0.4542 target = 0.199352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.159190 restraints weight = 8576.024| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.35 r_work: 0.3948 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7265 Z= 0.135 Angle : 0.666 6.864 10100 Z= 0.311 Chirality : 0.049 0.409 1171 Planarity : 0.005 0.052 1092 Dihedral : 10.971 75.251 1447 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.46 % Allowed : 13.21 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.30), residues: 715 helix: 0.02 (0.31), residues: 288 sheet: -1.83 (0.66), residues: 56 loop : -1.71 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1855 TYR 0.022 0.001 TYR A 946 PHE 0.020 0.002 PHE A 945 TRP 0.009 0.001 TRP A1048 HIS 0.004 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 7265) covalent geometry : angle 0.66618 / 0.31 (10100) hydrogen bonds : bond 0.04525 / 3.05 ( 233) hydrogen bonds : angle 4.95664 / 3.68 ( 634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.201 Fit side-chains REVERT: A 844 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: A 856 HIS cc_start: 0.6987 (m90) cc_final: 0.6675 (t-90) REVERT: A 1357 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.6615 (t80) REVERT: A 1808 MET cc_start: 0.6350 (mmp) cc_final: 0.6019 (mmp) REVERT: A 1859 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5997 (mp0) outliers start: 16 outliers final: 3 residues processed: 68 average time/residue: 0.0697 time to fit residues: 6.6492 Evaluate side-chains 60 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 14 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1549 HIS ** 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 = 0.4553 r_free = 0.4553 target = 0.200532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.160798 restraints weight = 8538.734| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.35 r_work: 0.3976 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7265 Z= 0.117 Angle : 0.630 6.603 10100 Z= 0.294 Chirality : 0.047 0.379 1171 Planarity : 0.005 0.051 1092 Dihedral : 10.727 74.591 1443 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.30 % Allowed : 14.13 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.30), residues: 715 helix: 0.43 (0.31), residues: 289 sheet: -1.79 (0.66), residues: 56 loop : -1.52 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1855 TYR 0.023 0.001 TYR A 946 PHE 0.016 0.002 PHE A 960 TRP 0.006 0.001 TRP A1024 HIS 0.003 0.001 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7265) covalent geometry : angle 0.63043 / 0.29 (10100) hydrogen bonds : bond 0.04204 / 2.85 ( 233) hydrogen bonds : angle 4.76832 / 3.53 ( 634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.218 Fit side-chains REVERT: A 844 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: A 856 HIS cc_start: 0.6993 (m90) cc_final: 0.6622 (t-90) REVERT: A 1320 ASP cc_start: 0.7347 (t70) cc_final: 0.6995 (t70) REVERT: A 1357 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6521 (t80) REVERT: A 1808 MET cc_start: 0.6364 (mmp) cc_final: 0.6036 (mmp) REVERT: A 1859 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6083 (mp0) outliers start: 15 outliers final: 6 residues processed: 69 average time/residue: 0.0759 time to fit residues: 7.1325 Evaluate side-chains 62 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1697 ILE Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1549 HIS ** 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 = 0.4486 r_free = 0.4486 target = 0.193679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.152220 restraints weight = 8690.073| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.34 r_work: 0.3863 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7265 Z= 0.223 Angle : 0.756 8.617 10100 Z= 0.354 Chirality : 0.054 0.481 1171 Planarity : 0.006 0.054 1092 Dihedral : 10.889 76.393 1443 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.61 % Allowed : 14.90 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.30), residues: 715 helix: -0.06 (0.30), residues: 288 sheet: -1.88 (0.68), residues: 56 loop : -1.54 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1855 TYR 0.031 0.002 TYR A 946 PHE 0.018 0.002 PHE A 896 TRP 0.007 0.002 TRP A1048 HIS 0.005 0.001 HIS A1727 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 7265) covalent geometry : angle 0.75630 / 0.35 (10100) hydrogen bonds : bond 0.05575 / 3.75 ( 233) hydrogen bonds : angle 5.26256 / 3.88 ( 634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.241 Fit side-chains REVERT: A 856 HIS cc_start: 0.7191 (m90) cc_final: 0.6802 (t-90) REVERT: A 1339 HIS cc_start: 0.5476 (OUTLIER) cc_final: 0.4925 (t-170) REVERT: A 1357 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6576 (t80) REVERT: A 1705 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5879 (pp20) REVERT: A 1859 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5955 (mp0) outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 0.0725 time to fit residues: 6.3221 Evaluate side-chains 67 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1041 HIS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1339 HIS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1859 GLU Chi-restraints excluded: chain A residue 1860 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1549 HIS ** 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 = 0.4525 r_free = 0.4525 target = 0.197731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.156565 restraints weight = 8518.369| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.33 r_work: 0.3921 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7265 Z= 0.144 Angle : 0.663 7.609 10100 Z= 0.309 Chirality : 0.049 0.344 1171 Planarity : 0.005 0.052 1092 Dihedral : 10.789 75.255 1443 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.84 % Allowed : 15.82 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.31), residues: 715 helix: 0.33 (0.31), residues: 282 sheet: -1.78 (0.69), residues: 56 loop : -1.45 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1855 TYR 0.027 0.001 TYR A 946 PHE 0.015 0.002 PHE A 960 TRP 0.007 0.001 TRP A1048 HIS 0.003 0.001 HIS A1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 7265) covalent geometry : angle 0.66329 / 0.31 (10100) hydrogen bonds : bond 0.04609 / 3.11 ( 233) hydrogen bonds : angle 4.98746 / 3.66 ( 634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.210 Fit side-chains REVERT: A 856 HIS cc_start: 0.7146 (m90) cc_final: 0.6746 (t-90) REVERT: A 1320 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7081 (t70) REVERT: A 1339 HIS cc_start: 0.5478 (OUTLIER) cc_final: 0.4866 (t-170) REVERT: A 1357 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6588 (t80) REVERT: A 1859 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5983 (mp0) outliers start: 12 outliers final: 6 residues processed: 61 average time/residue: 0.0683 time to fit residues: 5.9296 Evaluate side-chains 61 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1339 HIS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1859 GLU Chi-restraints excluded: chain A residue 1860 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 51 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.198550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.157469 restraints weight = 8569.556| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.39 r_work: 0.3939 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7265 Z= 0.134 Angle : 0.656 8.720 10100 Z= 0.305 Chirality : 0.048 0.338 1171 Planarity : 0.005 0.052 1092 Dihedral : 10.678 75.129 1443 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.15 % Allowed : 16.13 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.31), residues: 715 helix: 0.47 (0.31), residues: 283 sheet: -1.70 (0.71), residues: 56 loop : -1.35 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1855 TYR 0.026 0.001 TYR A 946 PHE 0.014 0.002 PHE A 960 TRP 0.006 0.001 TRP A1048 HIS 0.003 0.001 HIS A1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7265) covalent geometry : angle 0.65578 / 0.31 (10100) hydrogen bonds : bond 0.04416 / 2.99 ( 233) hydrogen bonds : angle 4.90170 / 3.60 ( 634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.223 Fit side-chains REVERT: A 856 HIS cc_start: 0.7152 (m90) cc_final: 0.6730 (t-90) REVERT: A 1357 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6599 (t80) REVERT: A 1705 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5493 (pp20) REVERT: A 1859 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5967 (mp0) outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.0808 time to fit residues: 6.8125 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1339 HIS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1859 GLU Chi-restraints excluded: chain A residue 1860 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.0010 chunk 40 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 766 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 = 0.4563 r_free = 0.4563 target = 0.201873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.161168 restraints weight = 8549.879| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.38 r_work: 0.3978 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7265 Z= 0.110 Angle : 0.628 7.677 10100 Z= 0.291 Chirality : 0.047 0.289 1171 Planarity : 0.005 0.051 1092 Dihedral : 10.564 75.196 1443 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.23 % Allowed : 17.67 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.31), residues: 715 helix: 0.74 (0.32), residues: 278 sheet: -1.70 (0.70), residues: 56 loop : -1.27 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1855 TYR 0.021 0.001 TYR A 946 PHE 0.012 0.001 PHE A 945 TRP 0.006 0.001 TRP A1048 HIS 0.003 0.001 HIS A 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 7265) covalent geometry : angle 0.62753 / 0.29 (10100) hydrogen bonds : bond 0.04041 / 2.74 ( 233) hydrogen bonds : angle 4.75166 / 3.50 ( 634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.247 Fit side-chains REVERT: A 856 HIS cc_start: 0.7109 (m90) cc_final: 0.6779 (t-90) REVERT: A 1357 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.6507 (t80) REVERT: A 1859 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6000 (mp0) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.0820 time to fit residues: 7.0516 Evaluate side-chains 59 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1689 HIS Chi-restraints excluded: chain A residue 1859 GLU Chi-restraints excluded: chain A residue 1860 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.200820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.160154 restraints weight = 8513.417| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.33 r_work: 0.3972 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7265 Z= 0.121 Angle : 0.638 8.195 10100 Z= 0.296 Chirality : 0.047 0.306 1171 Planarity : 0.005 0.051 1092 Dihedral : 10.446 75.242 1443 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.54 % Allowed : 17.36 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.31), residues: 715 helix: 0.63 (0.31), residues: 284 sheet: -1.73 (0.70), residues: 56 loop : -1.18 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1855 TYR 0.025 0.001 TYR A 946 PHE 0.014 0.001 PHE A 945 TRP 0.004 0.001 TRP A1048 HIS 0.003 0.001 HIS A1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7265) covalent geometry : angle 0.63771 / 0.30 (10100) hydrogen bonds : bond 0.04172 / 2.83 ( 233) hydrogen bonds : angle 4.79005 / 3.50 ( 634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.224 Fit side-chains REVERT: A 856 HIS cc_start: 0.7064 (m90) cc_final: 0.6674 (t-90) REVERT: A 1339 HIS cc_start: 0.5380 (OUTLIER) cc_final: 0.4848 (t-170) REVERT: A 1357 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6543 (t80) REVERT: A 1705 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5473 (pp20) REVERT: A 1859 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5909 (mp0) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.0721 time to fit residues: 6.5972 Evaluate side-chains 63 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1339 HIS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1689 HIS Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1859 GLU Chi-restraints excluded: chain A residue 1860 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.200851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.160086 restraints weight = 8507.076| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.37 r_work: 0.3966 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7265 Z= 0.124 Angle : 0.639 8.011 10100 Z= 0.297 Chirality : 0.047 0.292 1171 Planarity : 0.005 0.052 1092 Dihedral : 10.372 75.371 1443 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.38 % Allowed : 17.51 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.31), residues: 715 helix: 0.63 (0.31), residues: 284 sheet: -1.64 (0.71), residues: 56 loop : -1.16 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1855 TYR 0.025 0.001 TYR A 946 PHE 0.013 0.001 PHE A 945 TRP 0.005 0.001 TRP A1048 HIS 0.003 0.001 HIS A1339 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 7265) covalent geometry : angle 0.63930 / 0.30 (10100) hydrogen bonds : bond 0.04152 / 2.83 ( 233) hydrogen bonds : angle 4.76584 / 3.49 ( 634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.29 seconds wall clock time: 27 minutes 51.95 seconds (1671.95 seconds total)