Starting phenix.real_space_refine on Fri Aug 22 23:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyq_41728/08_2025/8tyq_41728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyq_41728/08_2025/8tyq_41728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tyq_41728/08_2025/8tyq_41728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyq_41728/08_2025/8tyq_41728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tyq_41728/08_2025/8tyq_41728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyq_41728/08_2025/8tyq_41728.map" } resolution = 2.99 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= 0.007 sd= 0.028 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 5484 2.51 5 N 1449 2.21 5 O 1544 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8529 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7645 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 957, 7635 Classifications: {'peptide': 957} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 913} Chain breaks: 24 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 957, 7635 Classifications: {'peptide': 957} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 43, 'TRANS': 913} Chain breaks: 24 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 7756 Chain: "B" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 845 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A1998 " occ=0.84 ... (18 atoms not shown) pdb=" NE2BHIS A1998 " occ=0.16 Time building chain proxies: 3.64, per 1000 atoms: 0.43 Number of scatterers: 8529 At special positions: 0 Unit cell: (82.28, 93.5, 144.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 F 3 9.00 O 1544 8.00 N 1449 7.00 C 5484 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: 0.96 Conformation dependent library (CDL) restraints added in 569.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 13 sheets defined 33.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 1346 through 1354 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1431 through 1437 removed outlier: 3.940A pdb=" N LEU A1435 " --> pdb=" O MET A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1457 Processing helix chain 'A' and resid 1458 through 1469 Processing helix chain 'A' and resid 1499 through 1508 Processing helix chain 'A' and resid 1563 through 1568 Processing helix chain 'A' and resid 1569 through 1579 Processing helix chain 'A' and resid 1631 through 1636 Processing helix chain 'A' and resid 1642 through 1646 Processing helix chain 'A' and resid 1651 through 1656 Processing helix chain 'A' and resid 1686 through 1688 No H-bonds generated for 'chain 'A' and resid 1686 through 1688' Processing helix chain 'A' and resid 1703 through 1712 removed outlier: 3.696A pdb=" N ARG A1707 " --> pdb=" O GLY A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1791 Processing helix chain 'A' and resid 1792 through 1796 Processing helix chain 'A' and resid 1830 through 1837 Processing helix chain 'A' and resid 1851 through 1855 Processing helix chain 'A' and resid 1871 through 1873 No H-bonds generated for 'chain 'A' and resid 1871 through 1873' Processing helix chain 'A' and resid 1884 through 1889 removed outlier: 3.713A pdb=" N ASP A1887 " --> pdb=" O LEU A1884 " (cutoff:3.500A) Processing helix chain 'A' and resid 1914 through 1925 Processing helix chain 'A' and resid 1954 through 1961 Processing helix chain 'A' and resid 1967 through 1988 removed outlier: 4.312A pdb=" N GLY A1981 " --> pdb=" O HIS A1977 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR A1984 " --> pdb=" O ASP A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2052 through 2068 Processing helix chain 'A' and resid 2094 through 2100 Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2118 through 2122 Processing helix chain 'A' and resid 2124 through 2133 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 3.762A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2280 No H-bonds generated for 'chain 'A' and resid 2278 through 2280' Processing helix chain 'A' and resid 2339 through 2344 Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2389 through 2396 removed outlier: 3.618A pdb=" N GLU A2395 " --> pdb=" O HIS A2391 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A2396 " --> pdb=" O PHE A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2525 Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.633A pdb=" N TYR B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.599A pdb=" N LEU B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 155' Processing sheet with id=AA1, first strand: chain 'A' and resid 1372 through 1376 removed outlier: 3.553A pdb=" N ASP A1372 " --> pdb=" O ASP A1394 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A1337 " --> pdb=" O ASN A1391 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A1393 " --> pdb=" O LEU A1337 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A1485 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A1449 " --> pdb=" O TYR A1485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1752 through 1753 removed outlier: 3.546A pdb=" N PHE A1762 " --> pdb=" O GLU A1753 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1763 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1730 through 1734 removed outlier: 3.836A pdb=" N GLY A1737 " --> pdb=" O TRP A1734 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AA5, first strand: chain 'A' and resid 1875 through 1877 removed outlier: 7.076A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AA7, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.882A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2152 through 2157 removed outlier: 4.233A pdb=" N CYS A2154 " --> pdb=" O GLY A2170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2199 through 2207 Processing sheet with id=AB1, first strand: chain 'A' and resid 2245 through 2249 removed outlier: 4.269A pdb=" N LYS A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2300 through 2304 removed outlier: 3.576A pdb=" N CYS A2302 " --> pdb=" O GLY A2318 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A2323 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A2335 " --> pdb=" O ILE A2323 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A2325 " --> pdb=" O GLN A2333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 3.688A pdb=" N THR A2356 " --> pdb=" O ALA A2366 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP A2377 " --> pdb=" O LEU A2383 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A2383 " --> pdb=" O ASP A2377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2414 through 2420 removed outlier: 6.831A pdb=" N GLY A2428 " --> pdb=" O LYS A2415 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A2417 " --> pdb=" O TRP A2426 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP A2426 " --> pdb=" O LEU A2417 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A2419 " --> pdb=" O ALA A2424 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A2424 " --> pdb=" O LEU A2419 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 927 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: 1.85 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1407 1.29 - 1.42: 2110 1.42 - 1.55: 5088 1.55 - 1.68: 8 1.68 - 1.81: 76 Bond restraints: 8689 Sorted by residual: bond pdb=" N PRO A2208 " pdb=" CD PRO A2208 " ideal model delta sigma weight residual 1.473 1.257 0.216 1.40e-02 5.10e+03 2.39e+02 bond pdb=" C23 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.456 1.277 0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C22 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.467 1.289 0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" C19 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.466 1.301 0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" C24 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.451 1.296 0.155 2.00e-02 2.50e+03 6.00e+01 ... (remaining 8684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.04: 11698 6.04 - 12.07: 46 12.07 - 18.11: 5 18.11 - 24.14: 0 24.14 - 30.18: 1 Bond angle restraints: 11750 Sorted by residual: angle pdb=" C TYR A1699 " pdb=" CA TYR A1699 " pdb=" CB TYR A1699 " ideal model delta sigma weight residual 109.66 79.48 30.18 1.94e+00 2.66e-01 2.42e+02 angle pdb=" C PHE A1700 " pdb=" N PRO A1701 " pdb=" CA PRO A1701 " ideal model delta sigma weight residual 119.84 132.02 -12.18 1.25e+00 6.40e-01 9.50e+01 angle pdb=" CA TYR A1695 " pdb=" C TYR A1695 " pdb=" N GLU A1696 " ideal model delta sigma weight residual 116.20 128.33 -12.13 1.25e+00 6.40e-01 9.41e+01 angle pdb=" CA TYR A1699 " pdb=" C TYR A1699 " pdb=" O TYR A1699 " ideal model delta sigma weight residual 121.46 110.80 10.66 1.17e+00 7.31e-01 8.29e+01 angle pdb=" N PRO A2208 " pdb=" CD PRO A2208 " pdb=" CG PRO A2208 " ideal model delta sigma weight residual 103.20 113.77 -10.57 1.50e+00 4.44e-01 4.97e+01 ... (remaining 11745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 4949 24.21 - 48.43: 252 48.43 - 72.64: 37 72.64 - 96.85: 6 96.85 - 121.07: 3 Dihedral angle restraints: 5247 sinusoidal: 2150 harmonic: 3097 Sorted by residual: dihedral pdb=" C TYR A1699 " pdb=" N TYR A1699 " pdb=" CA TYR A1699 " pdb=" CB TYR A1699 " ideal model delta harmonic sigma weight residual -122.60 -83.37 -39.23 0 2.50e+00 1.60e-01 2.46e+02 dihedral pdb=" N TYR A1699 " pdb=" C TYR A1699 " pdb=" CA TYR A1699 " pdb=" CB TYR A1699 " ideal model delta harmonic sigma weight residual 122.80 104.66 18.14 0 2.50e+00 1.60e-01 5.27e+01 dihedral pdb=" N GLU A1696 " pdb=" C GLU A1696 " pdb=" CA GLU A1696 " pdb=" CB GLU A1696 " ideal model delta harmonic sigma weight residual 122.80 105.23 17.57 0 2.50e+00 1.60e-01 4.94e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1296 0.103 - 0.206: 58 0.206 - 0.309: 3 0.309 - 0.413: 1 0.413 - 0.516: 2 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA TYR A1699 " pdb=" N TYR A1699 " pdb=" C TYR A1699 " pdb=" CB TYR A1699 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA GLU A1696 " pdb=" N GLU A1696 " pdb=" C GLU A1696 " pdb=" CB GLU A1696 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CB VAL A1946 " pdb=" CA VAL A1946 " pdb=" CG1 VAL A1946 " pdb=" CG2 VAL A1946 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1357 not shown) Planarity restraints: 1461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1941 " -0.083 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO A1942 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO A1942 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1942 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1700 " 0.060 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO A1701 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A1701 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A1701 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1695 " 0.031 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR A1695 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR A1695 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A1695 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A1695 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A1695 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A1695 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR A1695 " -0.014 2.00e-02 2.50e+03 ... (remaining 1458 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 581 2.74 - 3.28: 8281 3.28 - 3.82: 13609 3.82 - 4.36: 16855 4.36 - 4.90: 28325 Nonbonded interactions: 67651 Sorted by model distance: nonbonded pdb=" OG1 THR A2267 " pdb=" OD1 ASP A2269 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASP A2243 " pdb=" N SER A2244 " model vdw 2.205 3.120 nonbonded pdb=" O VAL A2152 " pdb=" OH TYR A2475 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A1419 " pdb=" OH TYR A1485 " model vdw 2.220 3.040 nonbonded pdb=" OD2 ASP A1962 " pdb=" OG SER A1965 " model vdw 2.244 3.040 ... (remaining 67646 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=0.16 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.410 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 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 0.216 8689 Z= 0.386 Angle : 0.977 30.180 11750 Z= 0.549 Chirality : 0.052 0.516 1360 Planarity : 0.007 0.123 1461 Dihedral : 14.458 121.065 3225 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.74 % Favored : 96.06 % Rotamer: Outliers : 0.53 % Allowed : 11.15 % Favored : 88.32 % Cbeta Deviations : 0.30 % 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 aren not related in a simple way. whole: -0.16 (0.27), residues: 1018 helix: 0.28 (0.30), residues: 312 sheet: 0.28 (0.35), residues: 211 loop : -0.42 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1895 TYR 0.059 0.003 TYR A1695 PHE 0.028 0.002 PHE A1700 TRP 0.025 0.002 TRP A2214 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00728 ( 8689) covalent geometry : angle 0.97703 (11750) hydrogen bonds : bond 0.14775 ( 342) hydrogen bonds : angle 6.70036 ( 927) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 233 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2214 TRP cc_start: 0.7542 (m100) cc_final: 0.7311 (m100) REVERT: B 43 ASN cc_start: 0.7276 (m-40) cc_final: 0.7042 (p0) outliers start: 5 outliers final: 2 residues processed: 236 average time/residue: 0.5323 time to fit residues: 134.4684 Evaluate side-chains 140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2295 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1342 ASN A1919 GLN A2295 ASN A2328 ASN A2433 HIS B 113 HIS B 137 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.151829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118938 restraints weight = 30353.255| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 4.62 r_work: 0.3641 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8689 Z= 0.189 Angle : 0.740 10.507 11750 Z= 0.369 Chirality : 0.048 0.192 1360 Planarity : 0.006 0.095 1461 Dihedral : 8.366 119.314 1151 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.50 % Allowed : 18.68 % Favored : 77.81 % 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 aren not related in a simple way. whole: -0.02 (0.27), residues: 1018 helix: 0.71 (0.30), residues: 300 sheet: 0.02 (0.33), residues: 244 loop : -0.40 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1628 TYR 0.021 0.002 TYR A2189 PHE 0.027 0.002 PHE A1700 TRP 0.021 0.002 TRP A2214 HIS 0.011 0.002 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 8689) covalent geometry : angle 0.73977 (11750) hydrogen bonds : bond 0.03852 ( 342) hydrogen bonds : angle 5.63470 ( 927) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.349 Fit side-chains REVERT: A 1419 TYR cc_start: 0.6758 (p90) cc_final: 0.6384 (p90) REVERT: A 1452 THR cc_start: 0.7973 (p) cc_final: 0.7608 (t) REVERT: A 1466 MET cc_start: 0.7990 (ptp) cc_final: 0.7774 (ppp) REVERT: A 1707 ARG cc_start: 0.7440 (tpp80) cc_final: 0.7219 (tpp-160) REVERT: A 1732 MET cc_start: 0.8306 (mpp) cc_final: 0.7814 (mpp) REVERT: A 1776 LEU cc_start: 0.7640 (mm) cc_final: 0.7344 (mt) REVERT: A 1788 MET cc_start: 0.8276 (mpp) cc_final: 0.8050 (mpp) REVERT: A 1824 LYS cc_start: 0.7213 (ptpt) cc_final: 0.6315 (mttp) REVERT: A 1895 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8257 (ttm110) REVERT: A 1903 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.6989 (m) REVERT: A 2214 TRP cc_start: 0.8380 (m100) cc_final: 0.8015 (m100) REVERT: A 2278 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8165 (ttpt) REVERT: A 2453 ASN cc_start: 0.7424 (t160) cc_final: 0.7181 (t160) REVERT: A 2459 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.6573 (pmm) REVERT: A 2505 GLN cc_start: 0.7151 (mt0) cc_final: 0.6912 (mm110) REVERT: B 43 ASN cc_start: 0.7626 (m-40) cc_final: 0.6930 (p0) REVERT: B 58 ASP cc_start: 0.6325 (m-30) cc_final: 0.5997 (m-30) outliers start: 32 outliers final: 9 residues processed: 180 average time/residue: 0.5206 time to fit residues: 100.2753 Evaluate side-chains 150 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1699 TYR Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2278 LYS Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2380 THR Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 0.0040 chunk 8 optimal weight: 9.9990 chunk 83 optimal weight: 0.0670 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1960 GLN A2053 GLN B 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.150564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.118637 restraints weight = 23123.097| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 4.10 r_work: 0.3639 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8689 Z= 0.139 Angle : 0.687 10.099 11750 Z= 0.342 Chirality : 0.046 0.199 1360 Planarity : 0.005 0.077 1461 Dihedral : 7.443 109.279 1151 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.40 % Allowed : 19.43 % Favored : 77.18 % 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 aren not related in a simple way. whole: 0.05 (0.27), residues: 1018 helix: 0.71 (0.30), residues: 302 sheet: 0.05 (0.34), residues: 237 loop : -0.30 (0.31), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1866 TYR 0.022 0.002 TYR A1419 PHE 0.019 0.002 PHE A2326 TRP 0.017 0.002 TRP A2214 HIS 0.009 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8689) covalent geometry : angle 0.68746 (11750) hydrogen bonds : bond 0.03540 ( 342) hydrogen bonds : angle 5.46907 ( 927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.246 Fit side-chains REVERT: A 1431 MET cc_start: 0.6238 (tmm) cc_final: 0.5655 (mtp) REVERT: A 1452 THR cc_start: 0.8047 (p) cc_final: 0.7673 (t) REVERT: A 1728 ARG cc_start: 0.5594 (mmt-90) cc_final: 0.5348 (mmt90) REVERT: A 1732 MET cc_start: 0.8082 (mpp) cc_final: 0.7871 (mpp) REVERT: A 1776 LEU cc_start: 0.7735 (mm) cc_final: 0.7467 (mt) REVERT: A 1895 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8204 (ttm110) REVERT: A 2214 TRP cc_start: 0.8432 (m100) cc_final: 0.8089 (m100) REVERT: A 2278 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7995 (tmmt) REVERT: A 2444 LEU cc_start: 0.8097 (tm) cc_final: 0.7809 (tp) REVERT: A 2453 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7206 (t160) REVERT: A 2459 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.6627 (pmm) REVERT: A 2505 GLN cc_start: 0.7268 (mt0) cc_final: 0.7030 (mm110) REVERT: B 43 ASN cc_start: 0.7792 (m-40) cc_final: 0.6887 (p0) outliers start: 31 outliers final: 12 residues processed: 163 average time/residue: 0.4774 time to fit residues: 83.6453 Evaluate side-chains 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1335 MET Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1699 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2278 LYS Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2453 ASN Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1960 GLN A2422 ASN B 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.148993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.115838 restraints weight = 29999.004| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 4.57 r_work: 0.3570 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8689 Z= 0.153 Angle : 0.702 9.882 11750 Z= 0.345 Chirality : 0.047 0.180 1360 Planarity : 0.005 0.069 1461 Dihedral : 7.438 110.326 1149 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.40 % Allowed : 19.11 % Favored : 77.49 % 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 aren not related in a simple way. whole: -0.09 (0.27), residues: 1018 helix: 0.60 (0.30), residues: 308 sheet: -0.11 (0.34), residues: 232 loop : -0.35 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2176 TYR 0.021 0.002 TYR A2189 PHE 0.014 0.002 PHE A1641 TRP 0.025 0.002 TRP A1811 HIS 0.005 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8689) covalent geometry : angle 0.70238 (11750) hydrogen bonds : bond 0.03515 ( 342) hydrogen bonds : angle 5.42788 ( 927) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.338 Fit side-chains REVERT: A 1373 VAL cc_start: 0.8530 (t) cc_final: 0.8329 (t) REVERT: A 1431 MET cc_start: 0.6277 (tmm) cc_final: 0.5694 (mtp) REVERT: A 1452 THR cc_start: 0.8048 (p) cc_final: 0.7634 (t) REVERT: A 1696 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7131 (mp0) REVERT: A 1707 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7149 (ttp-170) REVERT: A 1829 ASP cc_start: 0.7378 (m-30) cc_final: 0.7095 (m-30) REVERT: A 1869 MET cc_start: 0.7388 (mpp) cc_final: 0.7179 (mpp) REVERT: A 2214 TRP cc_start: 0.8481 (m100) cc_final: 0.8202 (m100) REVERT: A 2278 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7960 (tmmt) REVERT: A 2453 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7278 (t160) REVERT: A 2459 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.6769 (pmm) REVERT: B 43 ASN cc_start: 0.7763 (m-40) cc_final: 0.6885 (p0) REVERT: B 58 ASP cc_start: 0.6410 (m-30) cc_final: 0.6100 (m-30) outliers start: 31 outliers final: 12 residues processed: 145 average time/residue: 0.4923 time to fit residues: 76.8402 Evaluate side-chains 133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1840 LEU Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2278 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2453 ASN Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.149102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113903 restraints weight = 40759.061| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 6.22 r_work: 0.3509 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8689 Z= 0.138 Angle : 0.673 9.486 11750 Z= 0.332 Chirality : 0.045 0.239 1360 Planarity : 0.005 0.072 1461 Dihedral : 7.380 110.468 1149 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.72 % Allowed : 20.06 % Favored : 76.22 % 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 aren not related in a simple way. whole: -0.03 (0.27), residues: 1018 helix: 0.72 (0.30), residues: 302 sheet: -0.09 (0.34), residues: 231 loop : -0.35 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1866 TYR 0.020 0.002 TYR A2189 PHE 0.016 0.002 PHE A2326 TRP 0.014 0.001 TRP A2214 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8689) covalent geometry : angle 0.67293 (11750) hydrogen bonds : bond 0.03330 ( 342) hydrogen bonds : angle 5.30756 ( 927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.213 Fit side-chains REVERT: A 1431 MET cc_start: 0.6279 (tmm) cc_final: 0.5692 (mtp) REVERT: A 1452 THR cc_start: 0.8026 (p) cc_final: 0.7664 (t) REVERT: A 1696 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7277 (mp0) REVERT: A 1776 LEU cc_start: 0.8020 (mm) cc_final: 0.7734 (mt) REVERT: A 1789 GLU cc_start: 0.6898 (mp0) cc_final: 0.6651 (pm20) REVERT: A 1809 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7403 (ttpm) REVERT: A 2214 TRP cc_start: 0.8542 (m100) cc_final: 0.8252 (m100) REVERT: A 2444 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7957 (tp) REVERT: A 2453 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7311 (t160) REVERT: A 2459 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.6900 (pmm) REVERT: B 43 ASN cc_start: 0.7813 (m-40) cc_final: 0.6925 (p0) REVERT: B 58 ASP cc_start: 0.6338 (m-30) cc_final: 0.6023 (m-30) outliers start: 34 outliers final: 10 residues processed: 144 average time/residue: 0.4799 time to fit residues: 74.1098 Evaluate side-chains 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1809 LYS Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2444 LEU Chi-restraints excluded: chain A residue 2453 ASN Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 0.0970 chunk 75 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1929 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 = 0.4254 r_free = 0.4254 target = 0.148597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.115855 restraints weight = 37228.057| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 5.02 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8689 Z= 0.153 Angle : 0.678 9.687 11750 Z= 0.332 Chirality : 0.046 0.287 1360 Planarity : 0.005 0.076 1461 Dihedral : 7.389 110.323 1149 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.18 % Allowed : 20.81 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.27), residues: 1018 helix: 0.70 (0.30), residues: 302 sheet: -0.22 (0.34), residues: 233 loop : -0.32 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1895 TYR 0.021 0.002 TYR A2189 PHE 0.017 0.002 PHE A2326 TRP 0.016 0.002 TRP A2214 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8689) covalent geometry : angle 0.67799 (11750) hydrogen bonds : bond 0.03375 ( 342) hydrogen bonds : angle 5.22858 ( 927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.323 Fit side-chains REVERT: A 1431 MET cc_start: 0.6331 (tmm) cc_final: 0.5960 (mtp) REVERT: A 1452 THR cc_start: 0.8195 (p) cc_final: 0.7760 (t) REVERT: A 1745 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: A 1962 ASP cc_start: 0.7082 (t0) cc_final: 0.6845 (t0) REVERT: A 2453 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.7066 (t160) REVERT: A 2459 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.6652 (pmm) REVERT: B 58 ASP cc_start: 0.6349 (m-30) cc_final: 0.6014 (m-30) outliers start: 29 outliers final: 13 residues processed: 141 average time/residue: 0.4845 time to fit residues: 73.0785 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1745 GLU Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2278 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2444 LEU Chi-restraints excluded: chain A residue 2453 ASN Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.148484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.116734 restraints weight = 37360.122| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 5.03 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8689 Z= 0.150 Angle : 0.690 9.904 11750 Z= 0.338 Chirality : 0.046 0.259 1360 Planarity : 0.005 0.074 1461 Dihedral : 7.410 110.567 1149 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.65 % Allowed : 21.55 % Favored : 75.80 % 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 aren not related in a simple way. whole: -0.08 (0.27), residues: 1018 helix: 0.82 (0.30), residues: 296 sheet: -0.31 (0.34), residues: 231 loop : -0.35 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1735 TYR 0.021 0.002 TYR A2189 PHE 0.013 0.002 PHE A2262 TRP 0.016 0.001 TRP A2214 HIS 0.004 0.001 HIS A1928 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8689) covalent geometry : angle 0.69044 (11750) hydrogen bonds : bond 0.03381 ( 342) hydrogen bonds : angle 5.27410 ( 927) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.350 Fit side-chains REVERT: A 1431 MET cc_start: 0.6220 (tmm) cc_final: 0.5909 (mtp) REVERT: A 1452 THR cc_start: 0.8217 (p) cc_final: 0.7787 (t) REVERT: A 1702 MET cc_start: 0.6762 (mtm) cc_final: 0.6451 (mtp) REVERT: A 1929 HIS cc_start: 0.3884 (m-70) cc_final: 0.2714 (m-70) REVERT: A 1962 ASP cc_start: 0.7081 (t0) cc_final: 0.6880 (t0) REVERT: A 2459 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.6709 (pmm) REVERT: B 58 ASP cc_start: 0.6434 (m-30) cc_final: 0.6062 (m-30) outliers start: 24 outliers final: 14 residues processed: 130 average time/residue: 0.4966 time to fit residues: 69.2902 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2278 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2444 LEU Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 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 = 0.4248 r_free = 0.4248 target = 0.148187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.119121 restraints weight = 21599.357| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.60 r_work: 0.3612 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8689 Z= 0.155 Angle : 0.708 11.835 11750 Z= 0.349 Chirality : 0.046 0.289 1360 Planarity : 0.005 0.071 1461 Dihedral : 7.392 110.461 1149 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.55 % Allowed : 22.08 % Favored : 75.37 % 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 aren not related in a simple way. whole: -0.16 (0.27), residues: 1018 helix: 0.74 (0.30), residues: 296 sheet: -0.32 (0.35), residues: 231 loop : -0.42 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2176 TYR 0.021 0.002 TYR A2189 PHE 0.014 0.002 PHE A2262 TRP 0.016 0.001 TRP A2214 HIS 0.004 0.001 HIS A1928 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8689) covalent geometry : angle 0.70818 (11750) hydrogen bonds : bond 0.03478 ( 342) hydrogen bonds : angle 5.31718 ( 927) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.366 Fit side-chains REVERT: A 1431 MET cc_start: 0.6314 (tmm) cc_final: 0.5925 (mtp) REVERT: A 1452 THR cc_start: 0.8181 (p) cc_final: 0.7779 (t) REVERT: A 1702 MET cc_start: 0.6853 (mtm) cc_final: 0.6599 (mtp) REVERT: A 1776 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7881 (mt) REVERT: A 1929 HIS cc_start: 0.4365 (m-70) cc_final: 0.3220 (m-70) REVERT: A 2459 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.6953 (pmm) REVERT: B 58 ASP cc_start: 0.6541 (m-30) cc_final: 0.6160 (m-30) REVERT: B 137 HIS cc_start: 0.4947 (t-90) cc_final: 0.4362 (m90) outliers start: 23 outliers final: 14 residues processed: 126 average time/residue: 0.4871 time to fit residues: 65.9929 Evaluate side-chains 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1776 LEU Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2278 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2444 LEU Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1657 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.148076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.119355 restraints weight = 26522.806| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 4.98 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8689 Z= 0.160 Angle : 0.715 10.849 11750 Z= 0.350 Chirality : 0.046 0.245 1360 Planarity : 0.005 0.067 1461 Dihedral : 7.411 110.250 1149 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.44 % Allowed : 22.51 % Favored : 75.05 % 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 aren not related in a simple way. whole: -0.27 (0.27), residues: 1018 helix: 0.58 (0.30), residues: 302 sheet: -0.40 (0.34), residues: 231 loop : -0.44 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2176 TYR 0.022 0.002 TYR A2189 PHE 0.014 0.002 PHE A2262 TRP 0.016 0.001 TRP A2214 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8689) covalent geometry : angle 0.71518 (11750) hydrogen bonds : bond 0.03546 ( 342) hydrogen bonds : angle 5.35211 ( 927) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.339 Fit side-chains REVERT: A 1452 THR cc_start: 0.8255 (p) cc_final: 0.7830 (t) REVERT: A 1929 HIS cc_start: 0.3868 (m-70) cc_final: 0.2937 (m-70) REVERT: A 2459 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.6602 (pmm) REVERT: B 58 ASP cc_start: 0.6525 (m-30) cc_final: 0.6158 (m-30) REVERT: B 137 HIS cc_start: 0.5238 (t-90) cc_final: 0.4541 (m90) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.5055 time to fit residues: 68.6866 Evaluate side-chains 129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1732 MET Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2278 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2391 HIS Chi-restraints excluded: chain A residue 2444 LEU Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1437 ASN ** B 80 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 = 0.4247 r_free = 0.4247 target = 0.147943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.117146 restraints weight = 28859.257| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 4.28 r_work: 0.3593 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8689 Z= 0.152 Angle : 0.711 11.052 11750 Z= 0.349 Chirality : 0.046 0.254 1360 Planarity : 0.005 0.070 1461 Dihedral : 7.536 110.617 1149 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.12 % Allowed : 23.57 % Favored : 74.31 % 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 aren not related in a simple way. whole: -0.30 (0.27), residues: 1018 helix: 0.57 (0.30), residues: 302 sheet: -0.41 (0.35), residues: 226 loop : -0.48 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2176 TYR 0.021 0.002 TYR A2189 PHE 0.014 0.002 PHE A2262 TRP 0.015 0.002 TRP A2214 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8689) covalent geometry : angle 0.71136 (11750) hydrogen bonds : bond 0.03544 ( 342) hydrogen bonds : angle 5.37022 ( 927) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.351 Fit side-chains REVERT: A 1452 THR cc_start: 0.8156 (p) cc_final: 0.7782 (t) REVERT: A 1929 HIS cc_start: 0.4373 (m-70) cc_final: 0.3201 (m-70) REVERT: A 2459 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.6915 (pmm) REVERT: B 58 ASP cc_start: 0.6466 (m-30) cc_final: 0.6073 (m-30) outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.4460 time to fit residues: 59.4169 Evaluate side-chains 121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1700 PHE Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 VAL Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2278 LYS Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2391 HIS Chi-restraints excluded: chain A residue 2444 LEU Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 84 optimal weight: 0.0060 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.148578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.119738 restraints weight = 24752.102| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 4.17 r_work: 0.3593 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8689 Z= 0.142 Angle : 0.717 11.228 11750 Z= 0.349 Chirality : 0.046 0.244 1360 Planarity : 0.005 0.070 1461 Dihedral : 7.447 110.659 1149 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.12 % Allowed : 23.57 % Favored : 74.31 % 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 aren not related in a simple way. whole: -0.36 (0.27), residues: 1018 helix: 0.56 (0.30), residues: 302 sheet: -0.53 (0.34), residues: 230 loop : -0.48 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1735 TYR 0.021 0.002 TYR A2189 PHE 0.014 0.001 PHE A2262 TRP 0.016 0.001 TRP A2214 HIS 0.003 0.001 HIS A2510 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8689) covalent geometry : angle 0.71664 (11750) hydrogen bonds : bond 0.03445 ( 342) hydrogen bonds : angle 5.35945 ( 927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3200.18 seconds wall clock time: 55 minutes 14.19 seconds (3314.19 seconds total)