Starting phenix.real_space_refine on Fri May 16 22:43:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdp_43154/05_2025/8vdp_43154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdp_43154/05_2025/8vdp_43154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vdp_43154/05_2025/8vdp_43154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdp_43154/05_2025/8vdp_43154.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdp_43154/05_2025/8vdp_43154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdp_43154/05_2025/8vdp_43154.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 9077 2.51 5 N 2631 2.21 5 O 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14732 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2005, 14732 Classifications: {'peptide': 2005} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1926} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 8.22, per 1000 atoms: 0.56 Number of scatterers: 14732 At special positions: 0 Unit cell: (120.96, 130.176, 140.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2950 8.00 N 2631 7.00 C 9077 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: 4.34 Conformation dependent library (CDL) restraints added in 2.3 seconds 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 1 sheets defined 83.8% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.959A pdb=" N LEU A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.908A pdb=" N GLY A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.600A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 384 through 403 Processing helix chain 'A' and resid 489 through 512 removed outlier: 3.839A pdb=" N THR A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 525 through 562 Processing helix chain 'A' and resid 569 through 601 removed outlier: 3.817A pdb=" N GLU A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 626 Processing helix chain 'A' and resid 633 through 656 removed outlier: 4.102A pdb=" N LEU A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 693 Processing helix chain 'A' and resid 697 through 724 Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 729 through 756 Processing helix chain 'A' and resid 760 through 789 removed outlier: 3.698A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 789 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 815 Processing helix chain 'A' and resid 818 through 847 Processing helix chain 'A' and resid 849 through 880 Processing helix chain 'A' and resid 883 through 905 Processing helix chain 'A' and resid 907 through 941 removed outlier: 4.486A pdb=" N ALA A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 976 Proline residue: A 964 - end of helix Processing helix chain 'A' and resid 979 through 1008 removed outlier: 4.275A pdb=" N GLN A 995 " --> pdb=" O GLN A 991 " (cutoff:3.500A) Proline residue: A 996 - end of helix Processing helix chain 'A' and resid 1013 through 1045 Processing helix chain 'A' and resid 1051 through 1074 Processing helix chain 'A' and resid 1083 through 1111 Processing helix chain 'A' and resid 1115 through 1142 Processing helix chain 'A' and resid 1144 through 1175 removed outlier: 3.961A pdb=" N HIS A1175 " --> pdb=" O LYS A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1203 removed outlier: 3.627A pdb=" N LEU A1203 " --> pdb=" O CYS A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1225 removed outlier: 4.008A pdb=" N SER A1225 " --> pdb=" O LYS A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1260 Processing helix chain 'A' and resid 1263 through 1292 removed outlier: 3.680A pdb=" N GLY A1290 " --> pdb=" O VAL A1286 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A1292 " --> pdb=" O MET A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1325 Processing helix chain 'A' and resid 1328 through 1353 removed outlier: 3.568A pdb=" N LYS A1332 " --> pdb=" O SER A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1379 removed outlier: 4.678A pdb=" N ASN A1379 " --> pdb=" O GLU A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1417 Processing helix chain 'A' and resid 1418 through 1451 removed outlier: 3.715A pdb=" N ASP A1451 " --> pdb=" O VAL A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1483 Processing helix chain 'A' and resid 1487 through 1516 Processing helix chain 'A' and resid 1518 through 1545 Processing helix chain 'A' and resid 1551 through 1576 removed outlier: 3.961A pdb=" N ALA A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Proline residue: A1564 - end of helix Processing helix chain 'A' and resid 1578 through 1583 removed outlier: 4.487A pdb=" N SER A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1623 Proline residue: A1598 - end of helix Processing helix chain 'A' and resid 1626 through 1655 Processing helix chain 'A' and resid 1659 through 1684 removed outlier: 3.922A pdb=" N SER A1684 " --> pdb=" O LEU A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1722 removed outlier: 4.558A pdb=" N GLU A1714 " --> pdb=" O SER A1710 " (cutoff:3.500A) Proline residue: A1715 - end of helix Processing helix chain 'A' and resid 1724 through 1752 Proline residue: A1740 - end of helix Processing helix chain 'A' and resid 1754 through 1783 Processing helix chain 'A' and resid 1789 through 1821 removed outlier: 3.983A pdb=" N ALA A1821 " --> pdb=" O ALA A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1827 through 1840 Processing helix chain 'A' and resid 1849 through 1878 removed outlier: 4.288A pdb=" N TYR A1853 " --> pdb=" O SER A1849 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A1876 " --> pdb=" O VAL A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1881 through 1899 removed outlier: 3.588A pdb=" N LEU A1885 " --> pdb=" O GLU A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1907 Processing helix chain 'A' and resid 1909 through 1940 Processing helix chain 'A' and resid 1943 through 1970 removed outlier: 3.522A pdb=" N LYS A1947 " --> pdb=" O ASP A1943 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A1948 " --> pdb=" O VAL A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 2001 Processing helix chain 'A' and resid 2012 through 2037 Processing helix chain 'A' and resid 2040 through 2070 removed outlier: 3.739A pdb=" N LEU A2044 " --> pdb=" O SER A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2101 removed outlier: 3.782A pdb=" N GLN A2077 " --> pdb=" O ASP A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2136 removed outlier: 3.837A pdb=" N TRP A2112 " --> pdb=" O ASP A2108 " (cutoff:3.500A) Processing helix chain 'A' and resid 2137 through 2139 No H-bonds generated for 'chain 'A' and resid 2137 through 2139' Processing helix chain 'A' and resid 2140 through 2162 Processing helix chain 'A' and resid 2171 through 2196 removed outlier: 3.611A pdb=" N PHE A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2197 through 2224 removed outlier: 3.513A pdb=" N PHE A2224 " --> pdb=" O LYS A2220 " (cutoff:3.500A) Processing helix chain 'A' and resid 2229 through 2260 Processing helix chain 'A' and resid 2262 through 2290 removed outlier: 4.229A pdb=" N THR A2270 " --> pdb=" O LYS A2266 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY A2271 " --> pdb=" O GLN A2267 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A2290 " --> pdb=" O ALA A2286 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.838A pdb=" N GLN A 349 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 340 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 311 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS A 318 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER A 379 " --> pdb=" O LYS A 318 " (cutoff:3.500A) 1381 hydrogen bonds defined for protein. 4131 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: 6.23 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4633 1.33 - 1.45: 1440 1.45 - 1.57: 8715 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 14902 Sorted by residual: bond pdb=" N ASN A2262 " pdb=" CA ASN A2262 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.10e-03 1.21e+04 1.40e+01 bond pdb=" N VAL A 774 " pdb=" CA VAL A 774 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.32e+00 bond pdb=" N GLN A2259 " pdb=" CA GLN A2259 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.20e+00 bond pdb=" N ILE A 399 " pdb=" CA ILE A 399 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 8.94e+00 bond pdb=" N VAL A2254 " pdb=" CA VAL A2254 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.64e+00 ... (remaining 14897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 19595 1.94 - 3.89: 505 3.89 - 5.83: 76 5.83 - 7.78: 15 7.78 - 9.72: 4 Bond angle restraints: 20195 Sorted by residual: angle pdb=" CA ASN A2262 " pdb=" C ASN A2262 " pdb=" N PRO A2263 " ideal model delta sigma weight residual 118.16 122.72 -4.56 7.00e-01 2.04e+00 4.25e+01 angle pdb=" N ILE A1384 " pdb=" CA ILE A1384 " pdb=" C ILE A1384 " ideal model delta sigma weight residual 112.29 106.51 5.78 9.40e-01 1.13e+00 3.78e+01 angle pdb=" N PRO A2261 " pdb=" CA PRO A2261 " pdb=" C PRO A2261 " ideal model delta sigma weight residual 113.53 105.23 8.30 1.39e+00 5.18e-01 3.57e+01 angle pdb=" CA ASN A2262 " pdb=" C ASN A2262 " pdb=" O ASN A2262 " ideal model delta sigma weight residual 120.47 116.65 3.82 6.90e-01 2.10e+00 3.06e+01 angle pdb=" C GLU A 517 " pdb=" N THR A 518 " pdb=" CA THR A 518 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 ... (remaining 20190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8288 17.98 - 35.95: 806 35.95 - 53.93: 125 53.93 - 71.90: 55 71.90 - 89.87: 17 Dihedral angle restraints: 9291 sinusoidal: 3506 harmonic: 5785 Sorted by residual: dihedral pdb=" CA THR A 518 " pdb=" C THR A 518 " pdb=" N LEU A 519 " pdb=" CA LEU A 519 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA MET A1387 " pdb=" C MET A1387 " pdb=" N SER A1388 " pdb=" CA SER A1388 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA THR A 758 " pdb=" C THR A 758 " pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 9288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2156 0.067 - 0.133: 236 0.133 - 0.200: 19 0.200 - 0.266: 2 0.266 - 0.333: 1 Chirality restraints: 2414 Sorted by residual: chirality pdb=" CB THR A 518 " pdb=" CA THR A 518 " pdb=" OG1 THR A 518 " pdb=" CG2 THR A 518 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB VAL A 774 " pdb=" CA VAL A 774 " pdb=" CG1 VAL A 774 " pdb=" CG2 VAL A 774 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR A 772 " pdb=" N THR A 772 " pdb=" C THR A 772 " pdb=" CB THR A 772 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2411 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1655 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.81e+00 pdb=" N PRO A1656 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A1656 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1656 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A2171 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A2172 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A2172 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2172 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 976 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 977 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 977 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 977 " -0.028 5.00e-02 4.00e+02 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 178 2.66 - 3.22: 15458 3.22 - 3.78: 25229 3.78 - 4.34: 30413 4.34 - 4.90: 50078 Nonbonded interactions: 121356 Sorted by model distance: nonbonded pdb=" OD1 ASP A 233 " pdb=" N LYS A 234 " model vdw 2.097 3.120 nonbonded pdb=" OD2 ASP A1013 " pdb=" OG SER A1016 " model vdw 2.206 3.040 nonbonded pdb=" O GLY A1974 " pdb=" OG1 THR A1975 " model vdw 2.226 3.040 nonbonded pdb=" OE1 GLN A1111 " pdb=" NH2 ARG A1523 " model vdw 2.235 3.120 nonbonded pdb=" OG SER A1684 " pdb=" OE1 GLN A1686 " model vdw 2.241 3.040 ... (remaining 121351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.590 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: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 36.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14902 Z= 0.251 Angle : 0.735 9.719 20195 Z= 0.442 Chirality : 0.043 0.333 2414 Planarity : 0.004 0.065 2679 Dihedral : 15.348 89.875 5529 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.35 % Rotamer: Outliers : 0.71 % Allowed : 0.71 % Favored : 98.58 % 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: 2.39 (0.19), residues: 2001 helix: 2.35 (0.12), residues: 1610 sheet: -1.04 (0.83), residues: 39 loop : -1.92 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1630 HIS 0.004 0.001 HIS A1925 PHE 0.015 0.002 PHE A 516 TYR 0.020 0.002 TYR A1893 ARG 0.004 0.000 ARG A2275 Details of bonding type rmsd hydrogen bonds : bond 0.10866 ( 1381) hydrogen bonds : angle 4.92486 ( 4131) covalent geometry : bond 0.00492 (14902) covalent geometry : angle 0.73513 (20195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.709 Fit side-chains REVERT: A 780 GLU cc_start: 0.7893 (tt0) cc_final: 0.7177 (tt0) REVERT: A 1265 GLN cc_start: 0.7317 (tm-30) cc_final: 0.7014 (tm-30) REVERT: A 1998 PHE cc_start: 0.8894 (m-80) cc_final: 0.7992 (m-80) REVERT: A 2184 MET cc_start: 0.7375 (mmp) cc_final: 0.7095 (mmm) outliers start: 11 outliers final: 0 residues processed: 161 average time/residue: 0.2400 time to fit residues: 60.5397 Evaluate side-chains 112 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 181 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN A 381 GLN A 776 GLN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 GLN A1093 ASN A1250 ASN A1490 GLN A1554 ASN A1915 HIS ** A2046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2152 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.149140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110620 restraints weight = 26688.877| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.00 r_work: 0.3361 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14902 Z= 0.149 Angle : 0.595 8.947 20195 Z= 0.312 Chirality : 0.038 0.202 2414 Planarity : 0.004 0.058 2679 Dihedral : 4.557 26.467 2100 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.91 % Allowed : 7.89 % Favored : 91.20 % 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: 2.99 (0.19), residues: 2001 helix: 2.76 (0.12), residues: 1619 sheet: -0.27 (0.77), residues: 39 loop : -1.85 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1630 HIS 0.004 0.001 HIS A 283 PHE 0.010 0.001 PHE A1278 TYR 0.015 0.001 TYR A1893 ARG 0.003 0.000 ARG A2006 Details of bonding type rmsd hydrogen bonds : bond 0.04850 ( 1381) hydrogen bonds : angle 4.02103 ( 4131) covalent geometry : bond 0.00311 (14902) covalent geometry : angle 0.59546 (20195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.634 Fit side-chains REVERT: A 237 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: A 334 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8713 (mmmt) REVERT: A 780 GLU cc_start: 0.8166 (tt0) cc_final: 0.7448 (tt0) REVERT: A 899 MET cc_start: 0.8075 (tmm) cc_final: 0.7808 (tmm) REVERT: A 1265 GLN cc_start: 0.7357 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 1387 MET cc_start: 0.8082 (ppp) cc_final: 0.7685 (ppp) REVERT: A 1401 LYS cc_start: 0.7677 (tptp) cc_final: 0.7106 (pttp) REVERT: A 2017 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: A 2184 MET cc_start: 0.7715 (mmp) cc_final: 0.7383 (mmm) outliers start: 14 outliers final: 5 residues processed: 142 average time/residue: 0.2412 time to fit residues: 54.2455 Evaluate side-chains 120 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2019 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 55 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 50 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1736 GLN ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.149303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.110290 restraints weight = 26806.246| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.80 r_work: 0.3368 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14902 Z= 0.138 Angle : 0.546 8.273 20195 Z= 0.287 Chirality : 0.036 0.160 2414 Planarity : 0.004 0.052 2679 Dihedral : 4.341 22.928 2100 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.88 % Allowed : 10.48 % Favored : 87.65 % 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: 3.29 (0.19), residues: 2001 helix: 2.97 (0.12), residues: 1623 sheet: -0.71 (0.69), residues: 35 loop : -1.75 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1630 HIS 0.003 0.001 HIS A2152 PHE 0.011 0.001 PHE A 265 TYR 0.015 0.001 TYR A1893 ARG 0.003 0.000 ARG A2144 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 1381) hydrogen bonds : angle 3.78359 ( 4131) covalent geometry : bond 0.00292 (14902) covalent geometry : angle 0.54600 (20195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8120 (tt0) cc_final: 0.7166 (tt0) REVERT: A 899 MET cc_start: 0.8081 (tmm) cc_final: 0.7819 (tmm) REVERT: A 1043 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: A 1090 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8591 (m-30) REVERT: A 1265 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 1387 MET cc_start: 0.8140 (ppp) cc_final: 0.7557 (ppp) REVERT: A 1401 LYS cc_start: 0.7591 (tptp) cc_final: 0.7078 (pttp) REVERT: A 2017 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: A 2184 MET cc_start: 0.7714 (mmp) cc_final: 0.7385 (mmm) outliers start: 29 outliers final: 12 residues processed: 158 average time/residue: 0.2367 time to fit residues: 59.4982 Evaluate side-chains 128 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1824 VAL Chi-restraints excluded: chain A residue 1996 ILE Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 GLN ** 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 = 0.4099 r_free = 0.4099 target = 0.150037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110357 restraints weight = 26634.635| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.02 r_work: 0.3374 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14902 Z= 0.134 Angle : 0.538 8.621 20195 Z= 0.281 Chirality : 0.036 0.161 2414 Planarity : 0.004 0.052 2679 Dihedral : 4.244 20.377 2100 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.62 % Allowed : 12.42 % Favored : 85.96 % 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: 3.44 (0.19), residues: 2001 helix: 3.08 (0.12), residues: 1624 sheet: -0.74 (0.66), residues: 35 loop : -1.71 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1630 HIS 0.011 0.001 HIS A2152 PHE 0.012 0.001 PHE A 313 TYR 0.015 0.001 TYR A1893 ARG 0.006 0.000 ARG A2209 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 1381) hydrogen bonds : angle 3.69907 ( 4131) covalent geometry : bond 0.00287 (14902) covalent geometry : angle 0.53752 (20195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8147 (tt0) cc_final: 0.7245 (tt0) REVERT: A 899 MET cc_start: 0.8051 (tmm) cc_final: 0.7794 (tmm) REVERT: A 1043 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: A 1265 GLN cc_start: 0.7383 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 1401 LYS cc_start: 0.7584 (tptp) cc_final: 0.7089 (pttp) REVERT: A 2016 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7555 (mtp85) REVERT: A 2017 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: A 2184 MET cc_start: 0.7681 (mmp) cc_final: 0.7341 (mmm) outliers start: 25 outliers final: 15 residues processed: 136 average time/residue: 0.2431 time to fit residues: 52.5269 Evaluate side-chains 126 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1824 VAL Chi-restraints excluded: chain A residue 1979 ILE Chi-restraints excluded: chain A residue 1996 ILE Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 35 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 139 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 0.0870 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1921 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.150209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.111262 restraints weight = 26704.705| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.04 r_work: 0.3370 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14902 Z= 0.129 Angle : 0.530 8.039 20195 Z= 0.275 Chirality : 0.036 0.161 2414 Planarity : 0.004 0.051 2679 Dihedral : 4.189 24.314 2100 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.33 % Allowed : 12.74 % Favored : 84.93 % 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: 3.60 (0.19), residues: 2001 helix: 3.19 (0.12), residues: 1624 sheet: -0.79 (0.67), residues: 35 loop : -1.68 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1630 HIS 0.009 0.001 HIS A2152 PHE 0.012 0.001 PHE A 664 TYR 0.015 0.001 TYR A1893 ARG 0.005 0.000 ARG A2209 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1381) hydrogen bonds : angle 3.61164 ( 4131) covalent geometry : bond 0.00273 (14902) covalent geometry : angle 0.53015 (20195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 TRP cc_start: 0.8615 (p90) cc_final: 0.8303 (p90) REVERT: A 780 GLU cc_start: 0.8169 (tt0) cc_final: 0.7195 (tt0) REVERT: A 892 GLU cc_start: 0.8375 (tp30) cc_final: 0.8145 (tp30) REVERT: A 899 MET cc_start: 0.8049 (tmm) cc_final: 0.7788 (tmm) REVERT: A 915 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: A 1043 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: A 1265 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 1401 LYS cc_start: 0.7675 (tptp) cc_final: 0.7073 (pttp) REVERT: A 2016 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7648 (mtp85) REVERT: A 2017 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: A 2146 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8285 (pp) REVERT: A 2184 MET cc_start: 0.7725 (mmp) cc_final: 0.7377 (mmm) outliers start: 36 outliers final: 20 residues processed: 155 average time/residue: 0.2312 time to fit residues: 55.9715 Evaluate side-chains 139 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1824 VAL Chi-restraints excluded: chain A residue 1996 ILE Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2046 GLN Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2135 VAL Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 42 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** 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 = 0.4089 r_free = 0.4089 target = 0.149226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110328 restraints weight = 26741.935| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.05 r_work: 0.3349 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14902 Z= 0.142 Angle : 0.549 9.742 20195 Z= 0.284 Chirality : 0.036 0.165 2414 Planarity : 0.004 0.051 2679 Dihedral : 4.174 23.249 2100 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.13 % Allowed : 13.97 % Favored : 83.89 % 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: 3.62 (0.19), residues: 2001 helix: 3.20 (0.12), residues: 1626 sheet: -0.77 (0.69), residues: 35 loop : -1.66 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1630 HIS 0.008 0.001 HIS A2152 PHE 0.017 0.001 PHE A 313 TYR 0.015 0.001 TYR A1893 ARG 0.005 0.000 ARG A2209 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 1381) hydrogen bonds : angle 3.61805 ( 4131) covalent geometry : bond 0.00316 (14902) covalent geometry : angle 0.54946 (20195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8692 (mt-10) REVERT: A 359 TRP cc_start: 0.8653 (p90) cc_final: 0.8402 (p90) REVERT: A 780 GLU cc_start: 0.8146 (tt0) cc_final: 0.7224 (tt0) REVERT: A 899 MET cc_start: 0.8074 (tmm) cc_final: 0.7807 (tmm) REVERT: A 915 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: A 1043 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: A 1265 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7098 (tm-30) REVERT: A 1401 LYS cc_start: 0.7730 (tptp) cc_final: 0.7235 (pttp) REVERT: A 2016 ARG cc_start: 0.7978 (mtp-110) cc_final: 0.7604 (mtp85) REVERT: A 2017 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: A 2184 MET cc_start: 0.7729 (mmp) cc_final: 0.7383 (mmm) outliers start: 33 outliers final: 22 residues processed: 147 average time/residue: 0.2607 time to fit residues: 60.7159 Evaluate side-chains 140 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1824 VAL Chi-restraints excluded: chain A residue 1996 ILE Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2046 GLN Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2135 VAL Chi-restraints excluded: chain A residue 2143 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 118 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.149217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.110350 restraints weight = 26747.465| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.02 r_work: 0.3362 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14902 Z= 0.142 Angle : 0.551 8.725 20195 Z= 0.284 Chirality : 0.037 0.166 2414 Planarity : 0.004 0.051 2679 Dihedral : 4.155 22.777 2100 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.94 % Allowed : 14.55 % Favored : 83.51 % 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: 3.66 (0.19), residues: 2001 helix: 3.23 (0.12), residues: 1626 sheet: -0.61 (0.72), residues: 35 loop : -1.66 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 351 HIS 0.009 0.001 HIS A2152 PHE 0.012 0.001 PHE A 313 TYR 0.015 0.001 TYR A1893 ARG 0.004 0.000 ARG A2209 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 1381) hydrogen bonds : angle 3.60081 ( 4131) covalent geometry : bond 0.00316 (14902) covalent geometry : angle 0.55081 (20195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 TRP cc_start: 0.8625 (p90) cc_final: 0.8405 (p90) REVERT: A 780 GLU cc_start: 0.8185 (tt0) cc_final: 0.7280 (tt0) REVERT: A 899 MET cc_start: 0.8089 (tmm) cc_final: 0.7827 (tmm) REVERT: A 915 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: A 1043 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: A 1265 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7120 (tm-30) REVERT: A 1401 LYS cc_start: 0.7735 (tptp) cc_final: 0.7248 (pttp) REVERT: A 2016 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7730 (mtt90) REVERT: A 2017 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: A 2146 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8323 (pp) REVERT: A 2184 MET cc_start: 0.7722 (mmp) cc_final: 0.7370 (mmm) outliers start: 30 outliers final: 22 residues processed: 141 average time/residue: 0.2489 time to fit residues: 54.8807 Evaluate side-chains 142 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1824 VAL Chi-restraints excluded: chain A residue 1996 ILE Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2046 GLN Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2135 VAL Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.0050 chunk 33 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 159 optimal weight: 0.0670 chunk 98 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 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 = 0.4102 r_free = 0.4102 target = 0.150360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.111468 restraints weight = 26835.468| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.04 r_work: 0.3390 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14902 Z= 0.124 Angle : 0.539 9.991 20195 Z= 0.275 Chirality : 0.036 0.161 2414 Planarity : 0.004 0.050 2679 Dihedral : 4.101 23.716 2100 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.94 % Allowed : 14.42 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.80 (0.19), residues: 2001 helix: 3.32 (0.12), residues: 1628 sheet: -0.51 (0.73), residues: 35 loop : -1.65 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 351 HIS 0.009 0.001 HIS A2152 PHE 0.012 0.001 PHE A 313 TYR 0.015 0.001 TYR A1893 ARG 0.003 0.000 ARG A2144 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 1381) hydrogen bonds : angle 3.51598 ( 4131) covalent geometry : bond 0.00261 (14902) covalent geometry : angle 0.53889 (20195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 MET cc_start: 0.7922 (mtm) cc_final: 0.7609 (mtp) REVERT: A 780 GLU cc_start: 0.8107 (tt0) cc_final: 0.7264 (tt0) REVERT: A 861 LYS cc_start: 0.9163 (tmtt) cc_final: 0.8930 (tptt) REVERT: A 899 MET cc_start: 0.8035 (tmm) cc_final: 0.7809 (tmm) REVERT: A 915 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: A 1043 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: A 1265 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7047 (tm-30) REVERT: A 1352 MET cc_start: 0.7711 (ttm) cc_final: 0.7187 (ttm) REVERT: A 1401 LYS cc_start: 0.7652 (tptp) cc_final: 0.7189 (pttp) REVERT: A 2017 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: A 2184 MET cc_start: 0.7725 (mmp) cc_final: 0.7377 (mmm) outliers start: 30 outliers final: 22 residues processed: 153 average time/residue: 0.2544 time to fit residues: 60.1952 Evaluate side-chains 145 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1824 VAL Chi-restraints excluded: chain A residue 1828 VAL Chi-restraints excluded: chain A residue 1996 ILE Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2046 GLN Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2135 VAL Chi-restraints excluded: chain A residue 2143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 164 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 185 optimal weight: 8.9990 chunk 124 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: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 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 = 0.4095 r_free = 0.4095 target = 0.149740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.109336 restraints weight = 26618.418| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.03 r_work: 0.3362 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14902 Z= 0.135 Angle : 0.550 8.883 20195 Z= 0.283 Chirality : 0.037 0.168 2414 Planarity : 0.004 0.049 2679 Dihedral : 4.076 23.222 2100 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.81 % Allowed : 15.39 % Favored : 82.79 % 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: 3.78 (0.19), residues: 2001 helix: 3.29 (0.12), residues: 1629 sheet: -0.49 (0.75), residues: 35 loop : -1.58 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 359 HIS 0.004 0.001 HIS A2152 PHE 0.017 0.001 PHE A 313 TYR 0.014 0.001 TYR A1893 ARG 0.011 0.000 ARG A2016 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1381) hydrogen bonds : angle 3.53503 ( 4131) covalent geometry : bond 0.00297 (14902) covalent geometry : angle 0.55044 (20195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8366 (mm-30) REVERT: A 338 MET cc_start: 0.7946 (mtm) cc_final: 0.7653 (mtp) REVERT: A 780 GLU cc_start: 0.8182 (tt0) cc_final: 0.7283 (tt0) REVERT: A 861 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8926 (tptt) REVERT: A 899 MET cc_start: 0.8014 (tmm) cc_final: 0.7783 (tmm) REVERT: A 915 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: A 1043 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: A 1265 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7045 (tm-30) REVERT: A 1352 MET cc_start: 0.7714 (ttm) cc_final: 0.7186 (ttm) REVERT: A 1401 LYS cc_start: 0.7660 (tptp) cc_final: 0.7198 (pttp) REVERT: A 2017 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 2184 MET cc_start: 0.7721 (mmp) cc_final: 0.7369 (mmm) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.2527 time to fit residues: 56.5570 Evaluate side-chains 143 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1824 VAL Chi-restraints excluded: chain A residue 1828 VAL Chi-restraints excluded: chain A residue 1996 ILE Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2046 GLN Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2135 VAL Chi-restraints excluded: chain A residue 2143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 171 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 182 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.150470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.111291 restraints weight = 26800.104| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.90 r_work: 0.3390 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14902 Z= 0.128 Angle : 0.554 10.916 20195 Z= 0.282 Chirality : 0.036 0.167 2414 Planarity : 0.004 0.049 2679 Dihedral : 4.057 27.555 2100 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.55 % Allowed : 16.04 % Favored : 82.41 % 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: 3.87 (0.19), residues: 2001 helix: 3.36 (0.12), residues: 1628 sheet: -0.49 (0.75), residues: 35 loop : -1.53 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 359 HIS 0.003 0.001 HIS A2152 PHE 0.011 0.001 PHE A2160 TYR 0.015 0.001 TYR A1893 ARG 0.007 0.000 ARG A2016 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1381) hydrogen bonds : angle 3.50226 ( 4131) covalent geometry : bond 0.00276 (14902) covalent geometry : angle 0.55405 (20195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8811 (m-30) cc_final: 0.8404 (p0) REVERT: A 269 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8358 (mm-30) REVERT: A 338 MET cc_start: 0.7932 (mtm) cc_final: 0.7688 (mtp) REVERT: A 780 GLU cc_start: 0.8144 (tt0) cc_final: 0.7262 (tt0) REVERT: A 861 LYS cc_start: 0.9157 (tmtt) cc_final: 0.8846 (tptt) REVERT: A 899 MET cc_start: 0.8010 (tmm) cc_final: 0.7784 (tmm) REVERT: A 915 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: A 1040 LYS cc_start: 0.8202 (mmtp) cc_final: 0.7904 (mmtt) REVERT: A 1043 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: A 1265 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 1352 MET cc_start: 0.7676 (ttm) cc_final: 0.7119 (ttm) REVERT: A 1401 LYS cc_start: 0.7669 (tptp) cc_final: 0.7211 (pttp) REVERT: A 2017 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: A 2184 MET cc_start: 0.7711 (mmp) cc_final: 0.7359 (mmm) outliers start: 24 outliers final: 20 residues processed: 147 average time/residue: 0.2329 time to fit residues: 53.6596 Evaluate side-chains 141 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1437 THR Chi-restraints excluded: chain A residue 1824 VAL Chi-restraints excluded: chain A residue 1828 VAL Chi-restraints excluded: chain A residue 1996 ILE Chi-restraints excluded: chain A residue 2017 GLU Chi-restraints excluded: chain A residue 2046 GLN Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2135 VAL Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain A residue 2204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 147 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 128 optimal weight: 0.0770 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 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 = 0.4100 r_free = 0.4100 target = 0.150031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110572 restraints weight = 26641.607| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.92 r_work: 0.3375 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14902 Z= 0.140 Angle : 0.558 9.214 20195 Z= 0.287 Chirality : 0.037 0.168 2414 Planarity : 0.004 0.049 2679 Dihedral : 4.072 27.111 2100 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.75 % Allowed : 16.04 % Favored : 82.21 % 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: 3.81 (0.19), residues: 2001 helix: 3.31 (0.12), residues: 1628 sheet: -0.52 (0.77), residues: 35 loop : -1.53 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 359 HIS 0.003 0.001 HIS A1501 PHE 0.015 0.001 PHE A2175 TYR 0.019 0.001 TYR A1945 ARG 0.006 0.000 ARG A2016 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 1381) hydrogen bonds : angle 3.53237 ( 4131) covalent geometry : bond 0.00312 (14902) covalent geometry : angle 0.55771 (20195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6751.13 seconds wall clock time: 117 minutes 58.88 seconds (7078.88 seconds total)