Starting phenix.real_space_refine on Thu Mar 13 05:42:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyq_41728/03_2025/8tyq_41728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyq_41728/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tyq_41728/03_2025/8tyq_41728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyq_41728/03_2025/8tyq_41728.map" model { file = "/net/cci-nas-00/data/ceres_data/8tyq_41728/03_2025/8tyq_41728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyq_41728/03_2025/8tyq_41728.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.95, per 1000 atoms: 1.05 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: 2.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.15 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: 3.27 Time building geometry restraints manager: 2.51 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: 1.440 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.400 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.470 ------------------------------------------------------------------------------- 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= 0.462 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 : 13.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (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 TRP 0.025 0.002 TRP A2214 HIS 0.006 0.001 HIS B 54 PHE 0.028 0.002 PHE A1700 TYR 0.059 0.003 TYR A1695 ARG 0.005 0.000 ARG A1895 *********************** 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 : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2214 TRP cc_start: 0.7542 (m100) cc_final: 0.7310 (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: 1.0370 time to fit residues: 262.5224 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 : 0.920 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.0020 chunk 54 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1342 ASN ** A1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1919 GLN A2295 ASN A2328 ASN B 113 HIS B 137 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.154440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.122604 restraints weight = 24220.906| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 4.34 r_work: 0.3715 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8689 Z= 0.223 Angle : 0.719 10.378 11750 Z= 0.356 Chirality : 0.047 0.196 1360 Planarity : 0.006 0.095 1461 Dihedral : 7.580 107.354 1151 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.50 % Allowed : 18.26 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.27), residues: 1018 helix: 0.76 (0.30), residues: 300 sheet: -0.01 (0.33), residues: 241 loop : -0.35 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1791 HIS 0.013 0.002 HIS B 113 PHE 0.027 0.002 PHE A1700 TYR 0.023 0.002 TYR A1419 ARG 0.006 0.001 ARG A2176 *********************** 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 194 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.892 Fit side-chains REVERT: A 1452 THR cc_start: 0.7935 (p) cc_final: 0.7533 (t) REVERT: A 1466 MET cc_start: 0.8050 (ptp) cc_final: 0.7793 (ppp) REVERT: A 1732 MET cc_start: 0.8238 (mpp) cc_final: 0.7881 (mpp) REVERT: A 1776 LEU cc_start: 0.7453 (mm) cc_final: 0.7161 (mt) REVERT: A 1824 LYS cc_start: 0.7064 (ptpt) cc_final: 0.6254 (mttp) REVERT: A 1903 VAL cc_start: 0.7404 (OUTLIER) cc_final: 0.6799 (m) REVERT: A 2214 TRP cc_start: 0.8330 (m100) cc_final: 0.8025 (m100) REVERT: A 2234 LYS cc_start: 0.8078 (tptt) cc_final: 0.7820 (tttm) REVERT: A 2459 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.6478 (pmm) REVERT: A 2505 GLN cc_start: 0.6952 (mt0) cc_final: 0.6746 (mm110) REVERT: B 43 ASN cc_start: 0.7611 (m-40) cc_final: 0.6936 (p0) REVERT: B 58 ASP cc_start: 0.6356 (m-30) cc_final: 0.6098 (m-30) outliers start: 32 outliers final: 8 residues processed: 183 average time/residue: 1.1208 time to fit residues: 221.1557 Evaluate side-chains 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2295 ASN Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2053 GLN A2118 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 = 0.4277 r_free = 0.4277 target = 0.149856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.119481 restraints weight = 30009.719| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 4.68 r_work: 0.3616 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8689 Z= 0.262 Angle : 0.696 10.331 11750 Z= 0.345 Chirality : 0.047 0.224 1360 Planarity : 0.005 0.077 1461 Dihedral : 7.244 105.726 1150 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.61 % Allowed : 20.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.27), residues: 1018 helix: 0.62 (0.30), residues: 303 sheet: 0.05 (0.33), residues: 242 loop : -0.34 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A2214 HIS 0.008 0.001 HIS B 113 PHE 0.019 0.002 PHE A1890 TYR 0.020 0.002 TYR A2346 ARG 0.008 0.001 ARG A2176 *********************** 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 176 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.057 Fit side-chains REVERT: A 1450 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7889 (m) REVERT: A 1452 THR cc_start: 0.8112 (p) cc_final: 0.7722 (t) REVERT: A 1707 ARG cc_start: 0.7483 (tpp80) cc_final: 0.7200 (tpp-160) REVERT: A 1732 MET cc_start: 0.8194 (mpp) cc_final: 0.7858 (mpp) REVERT: A 1776 LEU cc_start: 0.7751 (mm) cc_final: 0.7480 (mt) REVERT: A 1788 MET cc_start: 0.8103 (mpp) cc_final: 0.7886 (mpp) REVERT: A 1789 GLU cc_start: 0.6346 (mp0) cc_final: 0.6137 (mp0) REVERT: A 1810 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7380 (mtpt) REVERT: A 2214 TRP cc_start: 0.8437 (m100) cc_final: 0.8072 (m100) REVERT: A 2234 LYS cc_start: 0.8026 (tptt) cc_final: 0.7765 (tttm) REVERT: A 2326 PHE cc_start: 0.6129 (m-80) cc_final: 0.5894 (m-80) REVERT: A 2453 ASN cc_start: 0.7544 (t160) cc_final: 0.7153 (t0) REVERT: A 2459 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.6643 (pmm) REVERT: A 2505 GLN cc_start: 0.7250 (mt0) cc_final: 0.6977 (mm110) REVERT: B 43 ASN cc_start: 0.7708 (m-40) cc_final: 0.6948 (p0) outliers start: 33 outliers final: 11 residues processed: 160 average time/residue: 1.1972 time to fit residues: 205.1788 Evaluate side-chains 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1699 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1810 LYS 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 2138 VAL Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2361 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 0.0270 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1960 GLN A2422 ASN A2433 HIS B 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.148619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.120253 restraints weight = 24114.115| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 4.32 r_work: 0.3580 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 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 = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8689 Z= 0.295 Angle : 0.719 9.877 11750 Z= 0.355 Chirality : 0.047 0.210 1360 Planarity : 0.005 0.070 1461 Dihedral : 7.373 110.275 1148 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.61 % Allowed : 20.28 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.27), residues: 1018 helix: 0.49 (0.30), residues: 309 sheet: -0.06 (0.34), residues: 230 loop : -0.49 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2214 HIS 0.005 0.001 HIS B 113 PHE 0.015 0.002 PHE A1890 TYR 0.017 0.002 TYR A2346 ARG 0.009 0.001 ARG A2339 *********************** 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 163 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 1431 MET cc_start: 0.6216 (tmm) cc_final: 0.5772 (mtp) REVERT: A 1452 THR cc_start: 0.8165 (p) cc_final: 0.7764 (t) REVERT: A 1733 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7850 (p90) REVERT: A 1829 ASP cc_start: 0.7532 (m-30) cc_final: 0.7245 (m-30) REVERT: A 2214 TRP cc_start: 0.8536 (m100) cc_final: 0.8192 (m100) REVERT: A 2444 LEU cc_start: 0.8152 (tm) cc_final: 0.7815 (tp) REVERT: A 2459 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.6893 (pmm) REVERT: B 43 ASN cc_start: 0.7871 (m-40) cc_final: 0.7073 (p0) REVERT: B 58 ASP cc_start: 0.6538 (m-30) cc_final: 0.6195 (m-30) outliers start: 33 outliers final: 13 residues processed: 151 average time/residue: 1.1032 time to fit residues: 179.4133 Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1690 ILE Chi-restraints excluded: chain A residue 1733 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 2138 VAL Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2361 THR 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 150 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 chunk 100 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.148898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.116986 restraints weight = 19073.742| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.95 r_work: 0.3660 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8689 Z= 0.246 Angle : 0.693 10.441 11750 Z= 0.338 Chirality : 0.046 0.229 1360 Planarity : 0.005 0.073 1461 Dihedral : 7.335 110.265 1148 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.29 % Allowed : 21.02 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 1018 helix: 0.55 (0.30), residues: 308 sheet: -0.16 (0.34), residues: 228 loop : -0.42 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2214 HIS 0.004 0.001 HIS B 80 PHE 0.017 0.002 PHE A2262 TYR 0.017 0.002 TYR A2346 ARG 0.008 0.001 ARG A1866 *********************** 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 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 1431 MET cc_start: 0.6304 (tmm) cc_final: 0.5878 (mtt) REVERT: A 1452 THR cc_start: 0.8158 (p) cc_final: 0.7761 (t) REVERT: A 1829 ASP cc_start: 0.7522 (m-30) cc_final: 0.7200 (m-30) REVERT: A 2214 TRP cc_start: 0.8413 (m100) cc_final: 0.8108 (m100) REVERT: A 2459 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.6848 (pmm) REVERT: B 43 ASN cc_start: 0.7880 (m-40) cc_final: 0.7088 (p0) REVERT: B 58 ASP cc_start: 0.6407 (m-30) cc_final: 0.6055 (m-30) outliers start: 30 outliers final: 13 residues processed: 136 average time/residue: 1.0251 time to fit residues: 150.2977 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 1840 LEU Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1922 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 2250 CYS Chi-restraints excluded: chain A residue 2361 THR Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** A2453 ASN ** 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 = 0.4246 r_free = 0.4246 target = 0.147767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.118959 restraints weight = 28391.661| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 5.03 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 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 = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.5524 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= 0.255 Angle : 0.695 9.793 11750 Z= 0.338 Chirality : 0.046 0.197 1360 Planarity : 0.005 0.074 1461 Dihedral : 7.289 109.980 1148 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.03 % Allowed : 21.02 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 1018 helix: 0.81 (0.30), residues: 296 sheet: -0.24 (0.34), residues: 231 loop : -0.40 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2214 HIS 0.004 0.001 HIS B 80 PHE 0.014 0.002 PHE A1890 TYR 0.016 0.002 TYR A2346 ARG 0.007 0.001 ARG A2176 *********************** 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 157 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 1.026 Fit side-chains REVERT: A 1431 MET cc_start: 0.6108 (tmm) cc_final: 0.5870 (mtt) REVERT: A 1452 THR cc_start: 0.8151 (p) cc_final: 0.7725 (t) REVERT: A 1714 GLU cc_start: 0.7552 (mp0) cc_final: 0.6650 (pm20) REVERT: A 1745 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: A 1776 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7637 (mt) REVERT: A 1929 HIS cc_start: 0.3851 (m-70) cc_final: 0.2710 (m-70) REVERT: A 2459 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.6432 (pmm) REVERT: B 58 ASP cc_start: 0.6421 (m-30) cc_final: 0.6064 (m-30) outliers start: 37 outliers final: 17 residues processed: 143 average time/residue: 0.9922 time to fit residues: 153.5055 Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 1745 GLU Chi-restraints excluded: chain A residue 1763 LEU 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 1991 ILE 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 2250 CYS 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 68 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 150 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1960 GLN B 43 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.148361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.119512 restraints weight = 25535.963| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 4.48 r_work: 0.3567 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8689 Z= 0.268 Angle : 0.726 10.167 11750 Z= 0.351 Chirality : 0.047 0.277 1360 Planarity : 0.006 0.083 1461 Dihedral : 7.324 110.446 1148 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.29 % Allowed : 22.51 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 1018 helix: 0.76 (0.30), residues: 296 sheet: -0.32 (0.34), residues: 231 loop : -0.40 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2496 HIS 0.007 0.001 HIS A1929 PHE 0.014 0.002 PHE A2262 TYR 0.016 0.002 TYR A2346 ARG 0.010 0.001 ARG A1735 *********************** 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: 30 poor density : 107 time to evaluate : 0.908 Fit side-chains REVERT: A 1431 MET cc_start: 0.6258 (tmm) cc_final: 0.5809 (mtt) REVERT: A 1452 THR cc_start: 0.8090 (p) cc_final: 0.7704 (t) REVERT: A 1714 GLU cc_start: 0.7770 (mp0) cc_final: 0.6812 (pm20) REVERT: A 1745 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: A 1776 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7876 (mt) REVERT: A 1789 GLU cc_start: 0.6741 (mp0) cc_final: 0.6539 (mp0) REVERT: A 1929 HIS cc_start: 0.4272 (m-70) cc_final: 0.3305 (m-70) REVERT: A 2459 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.6976 (pmm) REVERT: B 58 ASP cc_start: 0.6565 (m-30) cc_final: 0.6168 (m-30) outliers start: 30 outliers final: 16 residues processed: 125 average time/residue: 0.9795 time to fit residues: 133.0141 Evaluate side-chains 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 1745 GLU Chi-restraints excluded: chain A residue 1763 LEU 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 1991 ILE Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2278 LYS 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 150 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 102 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1960 GLN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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 = 0.4246 r_free = 0.4246 target = 0.148034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.114557 restraints weight = 41508.850| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 5.43 r_work: 0.3526 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8689 Z= 0.268 Angle : 0.726 10.167 11750 Z= 0.351 Chirality : 0.047 0.277 1360 Planarity : 0.006 0.083 1461 Dihedral : 7.324 110.446 1148 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.12 % Allowed : 24.10 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 1018 helix: 0.76 (0.30), residues: 296 sheet: -0.32 (0.34), residues: 231 loop : -0.40 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2496 HIS 0.007 0.001 HIS A1929 PHE 0.014 0.002 PHE A2262 TYR 0.016 0.002 TYR A2346 ARG 0.010 0.001 ARG A1735 *********************** 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 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.959 Fit side-chains REVERT: A 1431 MET cc_start: 0.6272 (tmm) cc_final: 0.5807 (mtt) REVERT: A 1452 THR cc_start: 0.8076 (p) cc_final: 0.7697 (t) REVERT: A 1714 GLU cc_start: 0.7808 (mp0) cc_final: 0.6857 (pm20) REVERT: A 1745 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: A 1776 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 1789 GLU cc_start: 0.6812 (mp0) cc_final: 0.6600 (mp0) REVERT: A 1929 HIS cc_start: 0.4319 (m-70) cc_final: 0.3339 (m-70) REVERT: A 2459 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7004 (pmm) REVERT: B 58 ASP cc_start: 0.6600 (m-30) cc_final: 0.6201 (m-30) outliers start: 19 outliers final: 16 residues processed: 118 average time/residue: 1.3040 time to fit residues: 167.9802 Evaluate side-chains 122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 1745 GLU Chi-restraints excluded: chain A residue 1763 LEU 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 1991 ILE Chi-restraints excluded: chain A residue 2138 VAL Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2278 LYS 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 150 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1960 GLN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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 = 0.4238 r_free = 0.4238 target = 0.147275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116020 restraints weight = 35179.526| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 4.89 r_work: 0.3548 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5788 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= 0.277 Angle : 0.730 10.930 11750 Z= 0.354 Chirality : 0.047 0.245 1360 Planarity : 0.005 0.075 1461 Dihedral : 7.355 109.961 1148 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.76 % Allowed : 23.35 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 1018 helix: 0.70 (0.30), residues: 297 sheet: -0.28 (0.34), residues: 229 loop : -0.47 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A2496 HIS 0.004 0.001 HIS A1929 PHE 0.014 0.002 PHE A1890 TYR 0.016 0.002 TYR A2346 ARG 0.008 0.001 ARG A2339 *********************** 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 131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.033 Fit side-chains REVERT: A 1431 MET cc_start: 0.6372 (tmm) cc_final: 0.5911 (mtp) REVERT: A 1452 THR cc_start: 0.8143 (p) cc_final: 0.7747 (t) REVERT: A 1702 MET cc_start: 0.6872 (mtm) cc_final: 0.6461 (mtp) REVERT: A 1714 GLU cc_start: 0.7722 (mp0) cc_final: 0.6917 (pm20) REVERT: A 1745 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7012 (tm-30) REVERT: A 1776 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7884 (mt) REVERT: A 1929 HIS cc_start: 0.4413 (m-70) cc_final: 0.3318 (m-70) REVERT: A 2459 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.6977 (pmm) REVERT: B 58 ASP cc_start: 0.6587 (m-30) cc_final: 0.6174 (m-30) outliers start: 25 outliers final: 15 residues processed: 124 average time/residue: 0.9747 time to fit residues: 131.5611 Evaluate side-chains 121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 1763 LEU 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 2138 VAL Chi-restraints excluded: chain A residue 2204 LEU Chi-restraints excluded: chain A residue 2247 CYS Chi-restraints excluded: chain A residue 2250 CYS Chi-restraints excluded: chain A residue 2278 LYS 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 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 39 optimal weight: 0.0770 chunk 23 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.148681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.120057 restraints weight = 24491.202| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 4.38 r_work: 0.3584 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8689 Z= 0.225 Angle : 0.730 11.172 11750 Z= 0.351 Chirality : 0.047 0.278 1360 Planarity : 0.005 0.075 1461 Dihedral : 7.344 110.543 1148 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.12 % Allowed : 23.67 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 1018 helix: 0.74 (0.30), residues: 297 sheet: -0.30 (0.34), residues: 228 loop : -0.50 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2214 HIS 0.006 0.001 HIS B 80 PHE 0.014 0.002 PHE A2262 TYR 0.018 0.002 TYR A2346 ARG 0.008 0.001 ARG A2176 ********************** 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 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.018 Fit side-chains REVERT: A 1431 MET cc_start: 0.6402 (tmm) cc_final: 0.5985 (mtp) REVERT: A 1452 THR cc_start: 0.8178 (p) cc_final: 0.7763 (t) REVERT: A 1651 LYS cc_start: 0.7651 (ptmt) cc_final: 0.7447 (tttp) REVERT: A 1702 MET cc_start: 0.6842 (mtm) cc_final: 0.6483 (mtp) REVERT: A 1714 GLU cc_start: 0.7690 (mp0) cc_final: 0.6928 (pm20) REVERT: A 1745 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7120 (tm-30) REVERT: A 1776 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7848 (mt) REVERT: A 1929 HIS cc_start: 0.4365 (m-70) cc_final: 0.3343 (m-70) REVERT: A 1944 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.5601 (pmm) REVERT: A 2326 PHE cc_start: 0.6393 (m-80) cc_final: 0.6043 (m-80) REVERT: A 2459 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.6838 (pmm) REVERT: B 58 ASP cc_start: 0.6499 (m-30) cc_final: 0.6072 (m-30) outliers start: 19 outliers final: 13 residues processed: 117 average time/residue: 0.9937 time to fit residues: 126.0915 Evaluate side-chains 120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1482 ILE 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 1944 MET 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 2250 CYS Chi-restraints excluded: chain A residue 2276 GLU Chi-restraints excluded: chain A residue 2278 LYS 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 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4247 r_free = 0.4247 target = 0.148323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.116629 restraints weight = 30067.781| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 4.04 r_work: 0.3579 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8689 Z= 0.239 Angle : 0.724 10.835 11750 Z= 0.351 Chirality : 0.047 0.260 1360 Planarity : 0.005 0.075 1461 Dihedral : 7.336 110.204 1148 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.02 % Allowed : 24.20 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.27), residues: 1018 helix: 0.59 (0.30), residues: 302 sheet: -0.23 (0.35), residues: 223 loop : -0.49 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2214 HIS 0.008 0.001 HIS B 80 PHE 0.014 0.002 PHE A2262 TYR 0.017 0.002 TYR A2346 ARG 0.008 0.001 ARG A2176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6921.15 seconds wall clock time: 121 minutes 17.04 seconds (7277.04 seconds total)