Starting phenix.real_space_refine on Thu Oct 22 23:41:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ybp_72756/10_2026/9ybp_72756.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ybp_72756/10_2026/9ybp_72756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ybp_72756/10_2026/9ybp_72756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ybp_72756/10_2026/9ybp_72756.map" model { file = "/net/cci-nas-00/data/ceres_data/9ybp_72756/10_2026/9ybp_72756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ybp_72756/10_2026/9ybp_72756.cif" } resolution = 4.0 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4175 2.51 5 N 1192 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6587 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 6587 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 941} Chain breaks: 20 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1377 Unresolved non-hydrogen angles: 1746 Unresolved non-hydrogen dihedrals: 1122 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 32, 'ARG:plan': 23, 'ASN:plan1': 22, 'GLU:plan': 42, 'TRP:plan': 2, 'PHE:plan': 13, 'TYR:plan': 12, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 734 Time building chain proxies: 1.53, per 1000 atoms: 0.23 Number of scatterers: 6587 At special positions: 0 Unit cell: (74.8, 90.695, 149.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1188 8.00 N 1192 7.00 C 4175 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: 0.51 Conformation dependent library (CDL) restraints added in 316.1 milliseconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 30.6% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 1424 through 1430 removed outlier: 3.550A pdb=" N VAL A1428 " --> pdb=" O GLY A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1441 removed outlier: 4.074A pdb=" N LYS A1439 " --> pdb=" O LEU A1435 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A1441 " --> pdb=" O ASN A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1474 removed outlier: 4.330A pdb=" N GLU A1472 " --> pdb=" O LYS A1468 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A1473 " --> pdb=" O ILE A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1477 No H-bonds generated for 'chain 'A' and resid 1475 through 1477' Processing helix chain 'A' and resid 1494 through 1509 removed outlier: 4.108A pdb=" N ASN A1506 " --> pdb=" O LYS A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1541 removed outlier: 4.107A pdb=" N GLU A1531 " --> pdb=" O TYR A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1560 removed outlier: 3.787A pdb=" N ASN A1560 " --> pdb=" O LEU A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1580 Processing helix chain 'A' and resid 1599 through 1613 removed outlier: 3.698A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A1610 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A1611 " --> pdb=" O MET A1607 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR A1612 " --> pdb=" O ALA A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1656 Processing helix chain 'A' and resid 1705 through 1715 Processing helix chain 'A' and resid 1770 through 1792 Processing helix chain 'A' and resid 1829 through 1833 Processing helix chain 'A' and resid 1856 through 1861 removed outlier: 4.260A pdb=" N ILE A1860 " --> pdb=" O ALA A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1870 removed outlier: 4.176A pdb=" N LEU A1870 " --> pdb=" O ARG A1866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1925 removed outlier: 4.120A pdb=" N GLU A1920 " --> pdb=" O LEU A1916 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.678A pdb=" N GLN A1960 " --> pdb=" O ASP A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1988 Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2052 through 2069 removed outlier: 3.788A pdb=" N VAL A2056 " --> pdb=" O GLN A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2079 removed outlier: 3.707A pdb=" N LYS A2078 " --> pdb=" O VAL A2074 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A2079 " --> pdb=" O GLU A2075 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2089 removed outlier: 4.008A pdb=" N ASP A2084 " --> pdb=" O PRO A2080 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A2086 " --> pdb=" O GLU A2082 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A2089 " --> pdb=" O GLU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2105 through 2115 removed outlier: 3.844A pdb=" N LYS A2109 " --> pdb=" O PRO A2105 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.549A pdb=" N SER A2134 " --> pdb=" O ASP A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2138 Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2389 through 2394 Processing helix chain 'A' and resid 2499 through 2504 Processing helix chain 'A' and resid 2504 through 2516 Processing sheet with id=AA1, first strand: chain 'A' and resid 1391 through 1395 removed outlier: 6.914A pdb=" N LEU A1337 " --> pdb=" O TRP A1393 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A1395 " --> pdb=" O LEU A1337 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A1339 " --> pdb=" O PHE A1395 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1414 " --> pdb=" O LYS A1336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1547 through 1548 Processing sheet with id=AA3, first strand: chain 'A' and resid 1730 through 1734 removed outlier: 3.805A pdb=" N PHE A1762 " --> pdb=" O GLU A1753 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1893 through 1898 removed outlier: 3.531A pdb=" N ALA A1937 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2001 through 2002 Processing sheet with id=AA6, first strand: chain 'A' and resid 2140 through 2143 removed outlier: 7.042A pdb=" N VAL A2495 " --> pdb=" O THR A2141 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS A2467 " --> pdb=" O LEU A2463 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A2463 " --> pdb=" O LYS A2467 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A2459 " --> pdb=" O LEU A2471 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A2457 " --> pdb=" O LEU A2473 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2156 through 2157 removed outlier: 3.978A pdb=" N VAL A2156 " --> pdb=" O TRP A2168 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP A2168 " --> pdb=" O VAL A2156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2225 through 2227 Processing sheet with id=AA9, first strand: chain 'A' and resid 2245 through 2247 removed outlier: 6.982A pdb=" N GLY A2266 " --> pdb=" O THR A2246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2271 through 2274 Processing sheet with id=AB2, first strand: chain 'A' and resid 2354 through 2358 removed outlier: 3.753A pdb=" N TYR A2364 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2414 through 2419 242 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2234 1.34 - 1.46: 1202 1.46 - 1.58: 3193 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6678 Sorted by residual: bond pdb=" N GLN A1879 " pdb=" CA GLN A1879 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.17e-02 7.31e+03 1.25e+01 bond pdb=" N PHE A1877 " pdb=" CA PHE A1877 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.22e-02 6.72e+03 1.22e+01 bond pdb=" N GLU A1878 " pdb=" CA GLU A1878 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.26e-02 6.30e+03 7.91e+00 bond pdb=" N ALA A1880 " pdb=" CA ALA A1880 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.02e+00 bond pdb=" C PHE A1479 " pdb=" N PRO A1480 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.69e+00 ... (remaining 6673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.21: 9097 6.21 - 12.42: 18 12.42 - 18.64: 3 18.64 - 24.85: 1 24.85 - 31.06: 3 Bond angle restraints: 9122 Sorted by residual: angle pdb=" N GLN A1879 " pdb=" CA GLN A1879 " pdb=" CB GLN A1879 " ideal model delta sigma weight residual 110.39 79.35 31.04 1.59e+00 3.96e-01 3.81e+02 angle pdb=" N PRO A1881 " pdb=" CA PRO A1881 " pdb=" C PRO A1881 " ideal model delta sigma weight residual 112.47 81.41 31.06 2.06e+00 2.36e-01 2.27e+02 angle pdb=" N GLN A1879 " pdb=" CA GLN A1879 " pdb=" C GLN A1879 " ideal model delta sigma weight residual 109.86 130.02 -20.16 1.55e+00 4.16e-01 1.69e+02 angle pdb=" C GLU A1878 " pdb=" CA GLU A1878 " pdb=" CB GLU A1878 " ideal model delta sigma weight residual 109.56 82.12 27.44 2.22e+00 2.03e-01 1.53e+02 angle pdb=" N PRO A1881 " pdb=" CA PRO A1881 " pdb=" CB PRO A1881 " ideal model delta sigma weight residual 103.25 115.90 -12.65 1.05e+00 9.07e-01 1.45e+02 ... (remaining 9117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 3652 18.03 - 36.05: 252 36.05 - 54.08: 37 54.08 - 72.10: 8 72.10 - 90.13: 5 Dihedral angle restraints: 3954 sinusoidal: 1091 harmonic: 2863 Sorted by residual: dihedral pdb=" N GLN A1879 " pdb=" C GLN A1879 " pdb=" CA GLN A1879 " pdb=" CB GLN A1879 " ideal model delta harmonic sigma weight residual 122.80 85.16 37.64 0 2.50e+00 1.60e-01 2.27e+02 dihedral pdb=" C GLU A1878 " pdb=" N GLU A1878 " pdb=" CA GLU A1878 " pdb=" CB GLU A1878 " ideal model delta harmonic sigma weight residual -122.60 -88.68 -33.92 0 2.50e+00 1.60e-01 1.84e+02 dihedral pdb=" C GLN A1879 " pdb=" N GLN A1879 " pdb=" CA GLN A1879 " pdb=" CB GLN A1879 " ideal model delta harmonic sigma weight residual -122.60 -95.33 -27.27 0 2.50e+00 1.60e-01 1.19e+02 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 1123 0.150 - 0.300: 7 0.300 - 0.450: 0 0.450 - 0.600: 1 0.600 - 0.750: 1 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CA ALA A1880 " pdb=" N ALA A1880 " pdb=" C ALA A1880 " pdb=" CB ALA A1880 " both_signs ideal model delta sigma weight residual False 2.48 3.23 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CA GLU A1878 " pdb=" N GLU A1878 " pdb=" C GLU A1878 " pdb=" CB GLU A1878 " both_signs ideal model delta sigma weight residual False 2.51 3.09 -0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" CB VAL A2469 " pdb=" CA VAL A2469 " pdb=" CG1 VAL A2469 " pdb=" CG2 VAL A2469 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 1129 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A1858 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" CG ASP A1858 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP A1858 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP A1858 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1856 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A1857 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1857 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1857 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1880 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ALA A1880 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A1880 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO A1881 " -0.014 2.00e-02 2.50e+03 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 56 2.62 - 3.19: 5634 3.19 - 3.76: 9675 3.76 - 4.33: 11801 4.33 - 4.90: 19359 Nonbonded interactions: 46525 Sorted by model distance: nonbonded pdb=" N PRO A1881 " pdb=" O PRO A1881 " model vdw 2.046 2.496 nonbonded pdb=" O GLN A1879 " pdb=" NE2 GLN A1879 " model vdw 2.164 3.120 nonbonded pdb=" OH TYR A1402 " pdb=" O HIS A1407 " model vdw 2.270 3.040 nonbonded pdb=" O ALA A1880 " pdb=" CB ALA A1880 " model vdw 2.319 2.768 nonbonded pdb=" OG SER A2166 " pdb=" O LEU A2182 " model vdw 2.320 3.040 ... (remaining 46520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.010 Normalize map: mean=0, sd=1: 2.110 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 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 : 0.004 0.043 6678 Z= 0.188 Angle : 1.065 31.061 9122 Z= 0.570 Chirality : 0.057 0.750 1132 Planarity : 0.006 0.063 1179 Dihedral : 13.349 90.129 2078 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.22 % Favored : 93.25 % Rotamer: Outliers : 0.20 % Allowed : 1.21 % Favored : 98.58 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 2.13 % 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: -2.49 (0.26), residues: 948 helix: -1.05 (0.30), residues: 270 sheet: -1.49 (0.41), residues: 151 loop : -2.05 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1918 TYR 0.013 0.001 TYR A2018 PHE 0.014 0.001 PHE A1700 TRP 0.037 0.002 TRP A1705 HIS 0.016 0.002 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 ( 6678) covalent geometry : angle 1.06510 / 0.57 ( 9122) hydrogen bonds : bond 0.17739 / 12.55 ( 242) hydrogen bonds : angle 6.96909 / 4.95 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 1404 THR cc_start: 0.8771 (t) cc_final: 0.8404 (m) REVERT: A 1736 GLN cc_start: 0.7974 (mm-40) cc_final: 0.6802 (tm-30) REVERT: A 1791 TRP cc_start: 0.7272 (m-90) cc_final: 0.6997 (m-90) REVERT: A 1984 TYR cc_start: 0.8321 (t80) cc_final: 0.8064 (t80) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.0680 time to fit residues: 9.5185 Evaluate side-chains 85 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0070 chunk 45 optimal weight: 0.0970 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2433 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.127141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.105344 restraints weight = 22527.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104919 restraints weight = 17173.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.105743 restraints weight = 16975.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.107020 restraints weight = 11922.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.107178 restraints weight = 10635.150| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6678 Z= 0.150 Angle : 0.636 7.391 9122 Z= 0.326 Chirality : 0.046 0.155 1132 Planarity : 0.005 0.053 1179 Dihedral : 4.316 18.705 1015 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.54 % Favored : 92.93 % Rotamer: Outliers : 1.42 % Allowed : 13.97 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.14 (0.26), residues: 948 helix: -0.49 (0.30), residues: 287 sheet: -1.39 (0.43), residues: 125 loop : -2.00 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1441 TYR 0.016 0.002 TYR A2018 PHE 0.018 0.002 PHE A1877 TRP 0.034 0.002 TRP A1705 HIS 0.009 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 6678) covalent geometry : angle 0.63645 / 0.33 ( 9122) hydrogen bonds : bond 0.03429 / 2.43 ( 242) hydrogen bonds : angle 5.37510 / 3.75 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 1404 THR cc_start: 0.8850 (t) cc_final: 0.8565 (m) REVERT: A 1719 MET cc_start: 0.6210 (tmm) cc_final: 0.6000 (tmm) REVERT: A 1791 TRP cc_start: 0.7223 (m-90) cc_final: 0.6873 (m-90) REVERT: A 1869 MET cc_start: 0.7403 (ptt) cc_final: 0.5954 (tpt) REVERT: A 1984 TYR cc_start: 0.8277 (t80) cc_final: 0.7824 (t80) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.0604 time to fit residues: 7.9762 Evaluate side-chains 82 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2452 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [45, 32, 64, 94, 1, 66, 8, 84, 53, 14, 73] chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 66 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 overall best weight: 2.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2510 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 = 0.4144 r_free = 0.4144 target = 0.123673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.102515 restraints weight = 22515.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.102580 restraints weight = 18161.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.102870 restraints weight = 17998.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.103037 restraints weight = 13119.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.104309 restraints weight = 11969.362| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6678 Z= 0.201 Angle : 0.685 7.683 9122 Z= 0.352 Chirality : 0.048 0.168 1132 Planarity : 0.005 0.056 1179 Dihedral : 4.702 20.322 1015 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.49 % Favored : 91.98 % Rotamer: Outliers : 2.83 % Allowed : 19.03 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.20 (0.26), residues: 948 helix: -0.43 (0.31), residues: 290 sheet: -1.48 (0.42), residues: 124 loop : -2.10 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1441 TYR 0.020 0.002 TYR A1984 PHE 0.022 0.002 PHE A1792 TRP 0.045 0.002 TRP A1705 HIS 0.011 0.002 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 6678) covalent geometry : angle 0.68532 / 0.35 ( 9122) hydrogen bonds : bond 0.03874 / 2.71 ( 242) hydrogen bonds : angle 5.68040 / 3.95 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 1719 MET cc_start: 0.6556 (tmm) cc_final: 0.6247 (tmm) REVERT: A 1791 TRP cc_start: 0.7221 (m-90) cc_final: 0.6973 (m-90) REVERT: A 1869 MET cc_start: 0.7344 (ptt) cc_final: 0.5761 (tpt) REVERT: A 1984 TYR cc_start: 0.8270 (t80) cc_final: 0.7915 (t80) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.0670 time to fit residues: 8.0917 Evaluate side-chains 79 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1660 LEU Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1875 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2061 LEU Chi-restraints excluded: chain A residue 2413 ARG Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2452 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [26, 70, 81, 23, 16, 73, 86, 37, 18, 36, 94] chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1928 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.120330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.098578 restraints weight = 23136.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.101067 restraints weight = 19096.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.100021 restraints weight = 18030.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100490 restraints weight = 12489.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.101705 restraints weight = 10602.290| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6678 Z= 0.279 Angle : 0.781 9.393 9122 Z= 0.403 Chirality : 0.050 0.187 1132 Planarity : 0.006 0.063 1179 Dihedral : 5.440 22.049 1015 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.39 % Favored : 90.08 % Rotamer: Outliers : 5.87 % Allowed : 20.45 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.26), residues: 948 helix: -0.59 (0.30), residues: 282 sheet: -1.38 (0.41), residues: 121 loop : -2.31 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1918 TYR 0.024 0.002 TYR A1984 PHE 0.020 0.002 PHE A1792 TRP 0.047 0.003 TRP A1705 HIS 0.011 0.002 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.28 ( 6678) covalent geometry : angle 0.78112 / 0.40 ( 9122) hydrogen bonds : bond 0.04351 / 2.99 ( 242) hydrogen bonds : angle 6.22354 / 4.32 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1585 PHE cc_start: 0.7682 (m-80) cc_final: 0.7385 (t80) REVERT: A 1656 PHE cc_start: 0.7768 (m-80) cc_final: 0.7524 (m-80) REVERT: A 1706 SER cc_start: 0.9109 (m) cc_final: 0.8836 (p) REVERT: A 1719 MET cc_start: 0.6627 (tmm) cc_final: 0.6223 (tmm) REVERT: A 1791 TRP cc_start: 0.7205 (m-90) cc_final: 0.6888 (m-90) REVERT: A 1869 MET cc_start: 0.7579 (ptt) cc_final: 0.5924 (tpt) REVERT: A 1944 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.5832 (ppp) outliers start: 29 outliers final: 20 residues processed: 98 average time/residue: 0.0608 time to fit residues: 8.7175 Evaluate side-chains 94 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1660 LEU Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1995 LEU Chi-restraints excluded: chain A residue 2061 LEU Chi-restraints excluded: chain A residue 2131 ILE Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2354 ILE Chi-restraints excluded: chain A residue 2413 ARG Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2452 CYS Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2510 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [59, 81, 33, 60, 31, 38, 98, 36, 22, 6, 20] chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 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 = 0.4133 r_free = 0.4133 target = 0.122945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.102209 restraints weight = 22966.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.102218 restraints weight = 19790.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.102507 restraints weight = 19937.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.102850 restraints weight = 13354.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.103889 restraints weight = 12004.130| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6678 Z= 0.146 Angle : 0.618 7.753 9122 Z= 0.319 Chirality : 0.046 0.161 1132 Planarity : 0.005 0.060 1179 Dihedral : 4.559 20.104 1015 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.96 % Favored : 92.51 % Rotamer: Outliers : 3.64 % Allowed : 24.49 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.15 (0.26), residues: 948 helix: -0.19 (0.31), residues: 283 sheet: -1.22 (0.43), residues: 123 loop : -2.26 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1441 TYR 0.016 0.001 TYR A1649 PHE 0.016 0.001 PHE A1704 TRP 0.027 0.002 TRP A1705 HIS 0.012 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6678) covalent geometry : angle 0.61769 / 0.32 ( 9122) hydrogen bonds : bond 0.03247 / 2.26 ( 242) hydrogen bonds : angle 5.42044 / 3.77 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1585 PHE cc_start: 0.7575 (m-80) cc_final: 0.7356 (t80) REVERT: A 1597 PHE cc_start: 0.7187 (m-80) cc_final: 0.6977 (t80) REVERT: A 1706 SER cc_start: 0.9100 (m) cc_final: 0.8737 (p) REVERT: A 1719 MET cc_start: 0.6588 (tmm) cc_final: 0.6090 (tmm) REVERT: A 1869 MET cc_start: 0.7292 (ptt) cc_final: 0.5646 (tpt) REVERT: A 1984 TYR cc_start: 0.8222 (t80) cc_final: 0.7835 (t80) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.0610 time to fit residues: 8.3204 Evaluate side-chains 82 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2061 LEU Chi-restraints excluded: chain A residue 2150 VAL Chi-restraints excluded: chain A residue 2413 ARG Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2452 CYS Chi-restraints excluded: chain A residue 2459 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [75, 2, 63, 30, 64, 12, 76, 91, 46, 69, 70] chunk 75 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1657 GLN ** A1676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.120509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.098671 restraints weight = 23206.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.100621 restraints weight = 19239.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.100438 restraints weight = 16663.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.100748 restraints weight = 11864.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.101316 restraints weight = 10671.082| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6678 Z= 0.220 Angle : 0.708 9.381 9122 Z= 0.359 Chirality : 0.048 0.166 1132 Planarity : 0.005 0.061 1179 Dihedral : 4.970 20.640 1015 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.39 % Favored : 90.08 % Rotamer: Outliers : 5.47 % Allowed : 24.49 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.25 (0.26), residues: 948 helix: -0.25 (0.30), residues: 282 sheet: -1.33 (0.43), residues: 123 loop : -2.30 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1918 TYR 0.021 0.002 TYR A1984 PHE 0.016 0.002 PHE A1792 TRP 0.023 0.002 TRP A1705 HIS 0.011 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 ( 6678) covalent geometry : angle 0.70819 / 0.36 ( 9122) hydrogen bonds : bond 0.03884 / 2.70 ( 242) hydrogen bonds : angle 5.79060 / 4.04 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1585 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7375 (t80) REVERT: A 1597 PHE cc_start: 0.7301 (m-80) cc_final: 0.6992 (t80) REVERT: A 1706 SER cc_start: 0.9145 (m) cc_final: 0.8853 (p) REVERT: A 1719 MET cc_start: 0.6609 (tmm) cc_final: 0.6020 (tmm) REVERT: A 1869 MET cc_start: 0.7431 (ptt) cc_final: 0.5812 (tpt) REVERT: A 1944 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.5749 (ppp) REVERT: A 2452 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7134 (t) outliers start: 27 outliers final: 17 residues processed: 91 average time/residue: 0.0623 time to fit residues: 8.3692 Evaluate side-chains 92 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1438 ILE Chi-restraints excluded: chain A residue 1585 PHE Chi-restraints excluded: chain A residue 1660 LEU Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1932 LEU Chi-restraints excluded: chain A residue 1935 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2061 LEU Chi-restraints excluded: chain A residue 2413 ARG Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2436 LEU Chi-restraints excluded: chain A residue 2452 CYS Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2493 LEU Chi-restraints excluded: chain A residue 2510 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [93, 61, 28, 42, 46, 25, 51, 48, 18, 75, 13] chunk 93 optimal weight: 0.3980 chunk 61 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 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 = 0.4137 r_free = 0.4137 target = 0.123261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.101336 restraints weight = 22957.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.100555 restraints weight = 17539.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.101340 restraints weight = 17406.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.102690 restraints weight = 12280.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.102754 restraints weight = 11055.414| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6678 Z= 0.123 Angle : 0.618 8.628 9122 Z= 0.310 Chirality : 0.046 0.165 1132 Planarity : 0.004 0.059 1179 Dihedral : 4.351 19.331 1015 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.22 % Favored : 93.25 % Rotamer: Outliers : 3.44 % Allowed : 26.72 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.27), residues: 948 helix: -0.03 (0.31), residues: 293 sheet: -1.13 (0.44), residues: 123 loop : -2.27 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1677 TYR 0.015 0.001 TYR A1649 PHE 0.019 0.001 PHE A1704 TRP 0.019 0.002 TRP A1705 HIS 0.012 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6678) covalent geometry : angle 0.61809 / 0.31 ( 9122) hydrogen bonds : bond 0.03062 / 2.15 ( 242) hydrogen bonds : angle 5.18951 / 3.63 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1585 PHE cc_start: 0.7708 (m-80) cc_final: 0.7421 (t80) REVERT: A 1597 PHE cc_start: 0.7303 (m-80) cc_final: 0.7082 (t80) REVERT: A 1706 SER cc_start: 0.9103 (m) cc_final: 0.8824 (p) REVERT: A 1869 MET cc_start: 0.7340 (ptt) cc_final: 0.5794 (tpt) REVERT: A 1944 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.5609 (ppp) REVERT: A 1984 TYR cc_start: 0.8274 (t80) cc_final: 0.7813 (t80) REVERT: A 2452 CYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6938 (t) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 0.0560 time to fit residues: 7.3289 Evaluate side-chains 89 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2061 LEU Chi-restraints excluded: chain A residue 2413 ARG Chi-restraints excluded: chain A residue 2417 LEU Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2452 CYS Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2510 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [55, 24, 61, 16, 44, 2, 30, 38, 31, 70, 98] chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1676 HIS A2510 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.124141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.102626 restraints weight = 22725.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.102242 restraints weight = 17483.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.102911 restraints weight = 17194.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.103245 restraints weight = 11785.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.103738 restraints weight = 11181.183| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6678 Z= 0.112 Angle : 0.617 9.345 9122 Z= 0.304 Chirality : 0.046 0.221 1132 Planarity : 0.004 0.057 1179 Dihedral : 4.093 19.125 1015 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.17 % Favored : 92.30 % Rotamer: Outliers : 2.83 % Allowed : 27.53 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.86 (0.27), residues: 948 helix: 0.24 (0.31), residues: 290 sheet: -1.01 (0.45), residues: 119 loop : -2.23 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2522 TYR 0.012 0.001 TYR A2018 PHE 0.009 0.001 PHE A1792 TRP 0.018 0.001 TRP A1811 HIS 0.012 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 6678) covalent geometry : angle 0.61686 / 0.30 ( 9122) hydrogen bonds : bond 0.02871 / 2.03 ( 242) hydrogen bonds : angle 4.98896 / 3.49 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1585 PHE cc_start: 0.7778 (m-80) cc_final: 0.7486 (t80) REVERT: A 1706 SER cc_start: 0.9065 (m) cc_final: 0.8840 (p) REVERT: A 1719 MET cc_start: 0.7989 (mpp) cc_final: 0.6134 (tmm) REVERT: A 1869 MET cc_start: 0.7282 (ptt) cc_final: 0.5604 (tpt) REVERT: A 1944 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.5542 (ppp) REVERT: A 1984 TYR cc_start: 0.8279 (t80) cc_final: 0.7796 (t80) REVERT: A 2452 CYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6969 (t) REVERT: A 2521 MET cc_start: 0.7624 (ppp) cc_final: 0.6901 (ppp) outliers start: 14 outliers final: 8 residues processed: 87 average time/residue: 0.0617 time to fit residues: 7.8418 Evaluate side-chains 86 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2061 LEU Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2452 CYS Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2510 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [26, 75, 72, 68, 56, 36, 5, 70, 54, 57, 82] chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 0.0030 chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 30.0000 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2502 HIS A2510 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.124880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.103540 restraints weight = 22824.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.103114 restraints weight = 17758.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.103866 restraints weight = 17213.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.104222 restraints weight = 11732.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.104707 restraints weight = 11115.306| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6678 Z= 0.102 Angle : 0.619 8.428 9122 Z= 0.302 Chirality : 0.046 0.196 1132 Planarity : 0.004 0.056 1179 Dihedral : 3.886 18.996 1015 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.12 % Favored : 93.35 % Rotamer: Outliers : 2.63 % Allowed : 28.74 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.70 (0.27), residues: 948 helix: 0.38 (0.32), residues: 283 sheet: -0.89 (0.46), residues: 121 loop : -2.11 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A2522 TYR 0.012 0.001 TYR A1649 PHE 0.021 0.001 PHE A1704 TRP 0.018 0.001 TRP A1811 HIS 0.017 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 6678) covalent geometry : angle 0.61873 / 0.30 ( 9122) hydrogen bonds : bond 0.02811 / 1.99 ( 242) hydrogen bonds : angle 4.85993 / 3.39 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1585 PHE cc_start: 0.7802 (m-80) cc_final: 0.7501 (t80) REVERT: A 1719 MET cc_start: 0.8005 (mpp) cc_final: 0.6026 (tmm) REVERT: A 1869 MET cc_start: 0.7215 (ptt) cc_final: 0.5565 (tpt) REVERT: A 1944 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.5499 (ppp) REVERT: A 1946 VAL cc_start: 0.7255 (OUTLIER) cc_final: 0.6614 (p) REVERT: A 1984 TYR cc_start: 0.8284 (t80) cc_final: 0.7785 (t80) REVERT: A 2421 LYS cc_start: 0.7321 (mmtt) cc_final: 0.6610 (mmmm) REVERT: A 2452 CYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7078 (t) REVERT: A 2521 MET cc_start: 0.7519 (ppp) cc_final: 0.6823 (ppp) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.0583 time to fit residues: 7.1298 Evaluate side-chains 88 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2061 LEU Chi-restraints excluded: chain A residue 2413 ARG Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2452 CYS Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2510 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [48, 75, 63, 54, 21, 30, 51, 8, 59, 35, 46] chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 8 optimal weight: 0.4980 chunk 59 optimal weight: 0.0040 chunk 35 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2502 HIS A2510 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.125411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.104342 restraints weight = 22505.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.103189 restraints weight = 15018.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.104100 restraints weight = 14267.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.104556 restraints weight = 10932.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.104713 restraints weight = 10307.846| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6678 Z= 0.099 Angle : 0.611 8.074 9122 Z= 0.297 Chirality : 0.046 0.182 1132 Planarity : 0.004 0.055 1179 Dihedral : 3.761 18.631 1015 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.70 % Favored : 93.78 % Rotamer: Outliers : 2.63 % Allowed : 28.54 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.52 (0.27), residues: 948 helix: 0.60 (0.32), residues: 271 sheet: -1.06 (0.45), residues: 132 loop : -1.92 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1677 TYR 0.011 0.001 TYR A1649 PHE 0.009 0.001 PHE A2129 TRP 0.017 0.001 TRP A1811 HIS 0.016 0.001 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6678) covalent geometry : angle 0.61085 / 0.30 ( 9122) hydrogen bonds : bond 0.02739 / 1.95 ( 242) hydrogen bonds : angle 4.77453 / 3.33 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1585 PHE cc_start: 0.7798 (m-80) cc_final: 0.7469 (t80) REVERT: A 1719 MET cc_start: 0.8011 (mpp) cc_final: 0.5913 (tmm) REVERT: A 1869 MET cc_start: 0.7124 (ptt) cc_final: 0.5594 (tpt) REVERT: A 1944 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.5482 (ppp) REVERT: A 1946 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6566 (p) REVERT: A 1984 TYR cc_start: 0.8235 (t80) cc_final: 0.7739 (t80) REVERT: A 2421 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6640 (mmmm) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.0637 time to fit residues: 7.5845 Evaluate side-chains 86 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1435 LEU Chi-restraints excluded: chain A residue 1732 MET Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2061 LEU Chi-restraints excluded: chain A residue 2413 ARG Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2471 LEU Chi-restraints excluded: chain A residue 2510 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [9, 92, 48, 38, 73, 3, 19, 26, 7, 49, 35] chunk 9 optimal weight: 10.0000 chunk 92 optimal weight: 0.1980 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 0.2980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2502 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.118891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.096962 restraints weight = 23324.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.096151 restraints weight = 20878.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.096609 restraints weight = 21079.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.098331 restraints weight = 14415.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.098426 restraints weight = 10674.903| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 6678 Z= 0.292 Angle : 0.814 10.012 9122 Z= 0.410 Chirality : 0.052 0.246 1132 Planarity : 0.005 0.060 1179 Dihedral : 5.204 22.641 1015 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.02 % Favored : 89.45 % Rotamer: Outliers : 2.63 % Allowed : 28.54 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.13 (0.27), residues: 948 helix: -0.15 (0.30), residues: 288 sheet: -1.30 (0.45), residues: 122 loop : -2.25 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1918 TYR 0.024 0.002 TYR A1984 PHE 0.026 0.002 PHE A1704 TRP 0.023 0.003 TRP A1811 HIS 0.017 0.002 HIS A2510 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.29 ( 6678) covalent geometry : angle 0.81413 / 0.41 ( 9122) hydrogen bonds : bond 0.04349 / 3.00 ( 242) hydrogen bonds : angle 6.05857 / 4.24 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1098.24 seconds wall clock time: 19 minutes 35.44 seconds (1175.44 seconds total)