Starting phenix.real_space_refine on Sat Mar 16 10:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/03_2024/7tdt_25838.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/03_2024/7tdt_25838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/03_2024/7tdt_25838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/03_2024/7tdt_25838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/03_2024/7tdt_25838.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/03_2024/7tdt_25838.pdb" } resolution = 4.0 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= 0.004 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 84 5.16 5 C 9352 2.51 5 N 2403 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A GLU 1645": "OE1" <-> "OE2" Residue "A GLU 1833": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14444 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1818, 14444 Classifications: {'peptide': 1818} Link IDs: {'PTRANS': 87, 'TRANS': 1730} Chain breaks: 10 Time building chain proxies: 7.29, per 1000 atoms: 0.50 Number of scatterers: 14444 At special positions: 0 Unit cell: (124, 219.48, 93, 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 84 16.00 O 2605 8.00 N 2403 7.00 C 9352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.05 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A1465 " - pdb=" SG CYS A1477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.73 Conformation dependent library (CDL) restraints added in 2.2 seconds 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 11 sheets defined 60.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 removed outlier: 4.120A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 46 removed outlier: 3.525A pdb=" N LEU A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.722A pdb=" N GLN A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.671A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 251 through 276 removed outlier: 4.218A pdb=" N ARG A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.164A pdb=" N ASP A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 368 through 380 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 408 through 429 Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 461 through 467 Processing helix chain 'A' and resid 483 through 504 removed outlier: 4.049A pdb=" N CYS A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 586 through 591 removed outlier: 4.429A pdb=" N TRP A 590 " --> pdb=" O MET A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 610 Processing helix chain 'A' and resid 630 through 665 Proline residue: A 641 - end of helix Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 677 through 706 Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 714 through 737 Processing helix chain 'A' and resid 742 through 759 Processing helix chain 'A' and resid 759 through 768 removed outlier: 4.298A pdb=" N LEU A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 780 removed outlier: 3.838A pdb=" N LYS A 776 " --> pdb=" O GLY A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 4.006A pdb=" N ALA A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 845 Processing helix chain 'A' and resid 939 through 948 Processing helix chain 'A' and resid 968 through 975 Processing helix chain 'A' and resid 991 through 1002 Processing helix chain 'A' and resid 1005 through 1019 removed outlier: 4.141A pdb=" N GLU A1011 " --> pdb=" O HIS A1007 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET A1012 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A1013 " --> pdb=" O LYS A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1028 Processing helix chain 'A' and resid 1037 through 1047 Processing helix chain 'A' and resid 1063 through 1079 removed outlier: 3.865A pdb=" N SER A1067 " --> pdb=" O VAL A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1097 removed outlier: 4.131A pdb=" N ASP A1095 " --> pdb=" O MET A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1123 removed outlier: 4.147A pdb=" N GLN A1121 " --> pdb=" O PHE A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1191 removed outlier: 3.661A pdb=" N HIS A1190 " --> pdb=" O LEU A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1232 removed outlier: 4.588A pdb=" N HIS A1223 " --> pdb=" O VAL A1219 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 3.879A pdb=" N ILE A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1342 Processing helix chain 'A' and resid 1343 through 1368 removed outlier: 4.634A pdb=" N ALA A1349 " --> pdb=" O LYS A1345 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN A1350 " --> pdb=" O GLY A1346 " (cutoff:3.500A) Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1400 through 1409 Processing helix chain 'A' and resid 1446 through 1451 Processing helix chain 'A' and resid 1505 through 1524 Processing helix chain 'A' and resid 1547 through 1561 Processing helix chain 'A' and resid 1569 through 1584 removed outlier: 3.524A pdb=" N PHE A1573 " --> pdb=" O SER A1569 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A1584 " --> pdb=" O PHE A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1618 Processing helix chain 'A' and resid 1639 through 1648 Processing helix chain 'A' and resid 1651 through 1666 Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 3.537A pdb=" N VAL A1681 " --> pdb=" O ILE A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1691 Processing helix chain 'A' and resid 1694 through 1724 removed outlier: 4.160A pdb=" N TYR A1698 " --> pdb=" O LYS A1694 " (cutoff:3.500A) Proline residue: A1713 - end of helix removed outlier: 3.861A pdb=" N PHE A1724 " --> pdb=" O ILE A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1753 removed outlier: 3.649A pdb=" N THR A1750 " --> pdb=" O GLY A1746 " (cutoff:3.500A) Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1755 through 1760 removed outlier: 3.668A pdb=" N VAL A1759 " --> pdb=" O PRO A1755 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A1760 " --> pdb=" O ALA A1756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1755 through 1760' Processing helix chain 'A' and resid 1765 through 1788 removed outlier: 4.230A pdb=" N LEU A1788 " --> pdb=" O ALA A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1809 removed outlier: 3.920A pdb=" N ILE A1809 " --> pdb=" O VAL A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1838 Processing helix chain 'A' and resid 1849 through 1874 removed outlier: 3.585A pdb=" N LEU A1853 " --> pdb=" O VAL A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2013 Processing helix chain 'A' and resid 2020 through 2033 removed outlier: 4.105A pdb=" N GLY A2025 " --> pdb=" O VAL A2021 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A2026 " --> pdb=" O GLY A2022 " (cutoff:3.500A) Processing helix chain 'A' and resid 2046 through 2059 removed outlier: 3.654A pdb=" N LYS A2050 " --> pdb=" O SER A2046 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A2059 " --> pdb=" O THR A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2094 Processing helix chain 'A' and resid 2103 through 2111 Processing helix chain 'A' and resid 2127 through 2135 Processing helix chain 'A' and resid 2148 through 2150 No H-bonds generated for 'chain 'A' and resid 2148 through 2150' Processing helix chain 'A' and resid 2151 through 2163 removed outlier: 3.664A pdb=" N VAL A2155 " --> pdb=" O ASP A2151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A2156 " --> pdb=" O LEU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2185 through 2202 removed outlier: 4.079A pdb=" N ARG A2189 " --> pdb=" O SER A2185 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A2190 " --> pdb=" O SER A2186 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG A2200 " --> pdb=" O GLN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2220 removed outlier: 3.599A pdb=" N PHE A2220 " --> pdb=" O VAL A2216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 5.857A pdb=" N GLY A 616 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A1592 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR A 618 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE A1594 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN A 620 " --> pdb=" O PHE A1594 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A1492 " --> pdb=" O ASP A1495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.631A pdb=" N HIS A 160 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 166 " --> pdb=" O HIS A 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 383 through 385 removed outlier: 6.319A pdb=" N LEU A 384 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 552 " --> pdb=" O THR A1630 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA7, first strand: chain 'A' and resid 928 through 929 removed outlier: 6.324A pdb=" N THR A 929 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A1054 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER A1087 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A1056 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS A 978 " --> pdb=" O ASP A1057 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.529A pdb=" N ILE A1101 " --> pdb=" O VAL A1112 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A1112 " --> pdb=" O ILE A1101 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A1103 " --> pdb=" O CYS A1110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1195 through 1200 removed outlier: 4.143A pdb=" N VAL A1197 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR A1205 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP A1199 " --> pdb=" O GLU A1203 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU A1203 " --> pdb=" O ASP A1199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2067 through 2068 Processing sheet with id=AB2, first strand: chain 'A' and resid 2171 through 2172 removed outlier: 3.993A pdb=" N LEU A2176 " --> pdb=" O VAL A2143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A2143 " --> pdb=" O LEU A2176 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A2205 " --> pdb=" O ARG A2144 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2283 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: 5.65 Time building geometry restraints manager: 6.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4563 1.35 - 1.47: 3542 1.47 - 1.59: 6540 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 14783 Sorted by residual: bond pdb=" CA PHE A 154 " pdb=" CB PHE A 154 " ideal model delta sigma weight residual 1.526 1.558 -0.032 1.51e-02 4.39e+03 4.38e+00 bond pdb=" C ASN A2149 " pdb=" N PRO A2150 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.93e+00 bond pdb=" N GLU A1005 " pdb=" CA GLU A1005 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.23e+00 bond pdb=" C THR A 645 " pdb=" O THR A 645 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.32e-02 5.74e+03 9.93e-01 bond pdb=" N TYR A1374 " pdb=" CA TYR A1374 " ideal model delta sigma weight residual 1.463 1.456 0.007 6.90e-03 2.10e+04 9.79e-01 ... (remaining 14778 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.50: 449 106.50 - 113.40: 8084 113.40 - 120.31: 5508 120.31 - 127.22: 5817 127.22 - 134.12: 191 Bond angle restraints: 20049 Sorted by residual: angle pdb=" C LYS A 137 " pdb=" CA LYS A 137 " pdb=" CB LYS A 137 " ideal model delta sigma weight residual 116.34 111.29 5.05 1.40e+00 5.10e-01 1.30e+01 angle pdb=" N VAL A1681 " pdb=" CA VAL A1681 " pdb=" C VAL A1681 " ideal model delta sigma weight residual 106.21 109.65 -3.44 1.07e+00 8.73e-01 1.04e+01 angle pdb=" CG ARG A2004 " pdb=" CD ARG A2004 " pdb=" NE ARG A2004 " ideal model delta sigma weight residual 112.00 119.07 -7.07 2.20e+00 2.07e-01 1.03e+01 angle pdb=" CA CYS A 54 " pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " ideal model delta sigma weight residual 114.40 120.89 -6.49 2.30e+00 1.89e-01 7.97e+00 angle pdb=" C GLU A1005 " pdb=" CA GLU A1005 " pdb=" CB GLU A1005 " ideal model delta sigma weight residual 110.42 115.77 -5.35 1.99e+00 2.53e-01 7.22e+00 ... (remaining 20044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 7992 17.41 - 34.83: 698 34.83 - 52.24: 121 52.24 - 69.66: 12 69.66 - 87.07: 13 Dihedral angle restraints: 8836 sinusoidal: 3552 harmonic: 5284 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 81 " pdb=" CB CYS A 81 " ideal model delta sinusoidal sigma weight residual -86.00 -2.19 -83.81 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CA CYS A 81 " pdb=" C CYS A 81 " pdb=" N PHE A 82 " pdb=" CA PHE A 82 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ASP A1064 " pdb=" C ASP A1064 " pdb=" N PRO A1065 " pdb=" CA PRO A1065 " ideal model delta harmonic sigma weight residual 180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1525 0.032 - 0.063: 513 0.063 - 0.095: 153 0.095 - 0.126: 75 0.126 - 0.158: 11 Chirality restraints: 2277 Sorted by residual: chirality pdb=" CA TRP A1436 " pdb=" N TRP A1436 " pdb=" C TRP A1436 " pdb=" CB TRP A1436 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE A1629 " pdb=" N ILE A1629 " pdb=" C ILE A1629 " pdb=" CB ILE A1629 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA PHE A1222 " pdb=" N PHE A1222 " pdb=" C PHE A1222 " pdb=" CB PHE A1222 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 2274 not shown) Planarity restraints: 2521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1064 " 0.056 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO A1065 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A1065 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A1065 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 995 " 0.019 2.00e-02 2.50e+03 1.55e-02 6.02e+00 pdb=" CG TRP A 995 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 995 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 995 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 995 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 995 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 995 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 995 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 995 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 995 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 67 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 68 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.024 5.00e-02 4.00e+02 ... (remaining 2518 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 123 2.51 - 3.10: 12024 3.10 - 3.70: 22712 3.70 - 4.30: 30486 4.30 - 4.90: 49295 Nonbonded interactions: 114640 Sorted by model distance: nonbonded pdb=" OH TYR A 385 " pdb=" OG1 THR A 392 " model vdw 1.908 2.440 nonbonded pdb=" OE1 GLN A1498 " pdb=" OH TYR A1508 " model vdw 1.952 2.440 nonbonded pdb=" OG1 THR A 483 " pdb=" OE1 GLU A 486 " model vdw 2.004 2.440 nonbonded pdb=" OE2 GLU A 967 " pdb=" OG SER A 969 " model vdw 2.085 2.440 nonbonded pdb=" O ASN A1734 " pdb=" NZ LYS A1824 " model vdw 2.099 2.520 ... (remaining 114635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 4.450 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.760 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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 : 0.002 0.046 14783 Z= 0.160 Angle : 0.572 7.069 20049 Z= 0.307 Chirality : 0.039 0.158 2277 Planarity : 0.004 0.085 2521 Dihedral : 13.402 87.069 5404 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.24 % Favored : 91.70 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.53 (0.20), residues: 1796 helix: 1.22 (0.17), residues: 992 sheet: -1.43 (0.47), residues: 121 loop : -2.64 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 995 HIS 0.005 0.001 HIS A2102 PHE 0.023 0.001 PHE A2009 TYR 0.020 0.001 TYR A1126 ARG 0.014 0.000 ARG A2004 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8247 (tp) cc_final: 0.7718 (pt) REVERT: A 513 ILE cc_start: 0.6339 (pt) cc_final: 0.6120 (pt) REVERT: A 644 MET cc_start: 0.7379 (ppp) cc_final: 0.6864 (ppp) REVERT: A 1744 LEU cc_start: 0.7925 (tt) cc_final: 0.7356 (tt) REVERT: A 1745 TYR cc_start: 0.7171 (t80) cc_final: 0.6825 (t80) REVERT: A 1833 GLU cc_start: 0.7843 (pp20) cc_final: 0.7454 (pp20) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2264 time to fit residues: 101.3965 Evaluate side-chains 223 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN A1686 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14783 Z= 0.212 Angle : 0.683 8.862 20049 Z= 0.340 Chirality : 0.044 0.210 2277 Planarity : 0.005 0.079 2521 Dihedral : 4.412 24.385 1943 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 1.12 % Allowed : 10.97 % Favored : 87.91 % 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: -0.65 (0.20), residues: 1796 helix: 1.06 (0.16), residues: 1018 sheet: -1.69 (0.44), residues: 136 loop : -2.67 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 995 HIS 0.007 0.001 HIS A2006 PHE 0.031 0.002 PHE A2158 TYR 0.018 0.002 TYR A1767 ARG 0.008 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8314 (tp) cc_final: 0.7737 (pt) REVERT: A 73 ILE cc_start: 0.8737 (pt) cc_final: 0.8523 (pt) REVERT: A 275 MET cc_start: 0.8456 (ppp) cc_final: 0.8214 (ppp) REVERT: A 396 MET cc_start: 0.7142 (tmm) cc_final: 0.6826 (tmm) REVERT: A 644 MET cc_start: 0.7382 (ppp) cc_final: 0.6848 (ppp) REVERT: A 696 SER cc_start: 0.8851 (t) cc_final: 0.8518 (p) REVERT: A 1377 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4931 (mm) REVERT: A 1745 TYR cc_start: 0.7360 (t80) cc_final: 0.6971 (t80) REVERT: A 1833 GLU cc_start: 0.7792 (pp20) cc_final: 0.7520 (pp20) outliers start: 18 outliers final: 14 residues processed: 247 average time/residue: 0.2192 time to fit residues: 85.1945 Evaluate side-chains 238 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1642 GLN A1686 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14783 Z= 0.188 Angle : 0.668 12.296 20049 Z= 0.329 Chirality : 0.043 0.193 2277 Planarity : 0.004 0.076 2521 Dihedral : 4.427 24.379 1943 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.56 % Allowed : 13.84 % Favored : 84.60 % 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: -0.78 (0.20), residues: 1796 helix: 0.90 (0.16), residues: 1023 sheet: -1.45 (0.47), residues: 128 loop : -2.72 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 995 HIS 0.005 0.001 HIS A2006 PHE 0.029 0.001 PHE A2158 TYR 0.021 0.001 TYR A1710 ARG 0.007 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 249 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8299 (tp) cc_final: 0.7743 (pt) REVERT: A 73 ILE cc_start: 0.8690 (pt) cc_final: 0.8478 (pt) REVERT: A 382 LYS cc_start: 0.8369 (mmtp) cc_final: 0.8133 (tppt) REVERT: A 644 MET cc_start: 0.7571 (ppp) cc_final: 0.7170 (ppp) REVERT: A 728 VAL cc_start: 0.8773 (t) cc_final: 0.8442 (p) REVERT: A 931 PHE cc_start: 0.8254 (t80) cc_final: 0.7964 (t80) REVERT: A 1377 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.5184 (mm) REVERT: A 1558 MET cc_start: 0.8550 (tmm) cc_final: 0.8213 (tmm) REVERT: A 1745 TYR cc_start: 0.7337 (t80) cc_final: 0.6815 (t80) REVERT: A 1833 GLU cc_start: 0.7823 (pp20) cc_final: 0.7605 (pp20) REVERT: A 2157 ASP cc_start: 0.8301 (m-30) cc_final: 0.8075 (m-30) REVERT: A 2178 TYR cc_start: 0.7423 (m-10) cc_final: 0.7160 (m-10) outliers start: 25 outliers final: 16 residues processed: 259 average time/residue: 0.2276 time to fit residues: 93.0842 Evaluate side-chains 243 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 174 optimal weight: 9.9990 chunk 86 optimal weight: 0.0010 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 404 GLN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14783 Z= 0.244 Angle : 0.687 10.085 20049 Z= 0.343 Chirality : 0.044 0.176 2277 Planarity : 0.005 0.073 2521 Dihedral : 4.537 24.528 1943 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 2.62 % Allowed : 16.27 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.92 (0.20), residues: 1796 helix: 0.77 (0.16), residues: 1023 sheet: -1.53 (0.47), residues: 128 loop : -2.75 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 995 HIS 0.005 0.001 HIS A2006 PHE 0.026 0.002 PHE A2158 TYR 0.018 0.002 TYR A1767 ARG 0.005 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8409 (tp) cc_final: 0.7784 (pt) REVERT: A 275 MET cc_start: 0.8628 (ppp) cc_final: 0.8404 (ppp) REVERT: A 396 MET cc_start: 0.7192 (tmm) cc_final: 0.6740 (tmm) REVERT: A 644 MET cc_start: 0.7513 (ppp) cc_final: 0.7160 (ppp) REVERT: A 728 VAL cc_start: 0.8820 (t) cc_final: 0.8475 (p) REVERT: A 945 ILE cc_start: 0.7275 (pt) cc_final: 0.6955 (tp) REVERT: A 1239 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 2157 ASP cc_start: 0.7781 (m-30) cc_final: 0.7466 (m-30) outliers start: 42 outliers final: 29 residues processed: 249 average time/residue: 0.2229 time to fit residues: 88.4706 Evaluate side-chains 244 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1858 VAL Chi-restraints excluded: chain A residue 2055 THR Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 149 optimal weight: 0.0050 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 404 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN A1686 HIS ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14783 Z= 0.174 Angle : 0.678 11.239 20049 Z= 0.331 Chirality : 0.043 0.179 2277 Planarity : 0.004 0.064 2521 Dihedral : 4.464 24.520 1943 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.56 % Allowed : 18.02 % Favored : 79.43 % 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: -0.93 (0.20), residues: 1796 helix: 0.76 (0.16), residues: 1027 sheet: -1.51 (0.47), residues: 134 loop : -2.78 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 995 HIS 0.005 0.001 HIS A2006 PHE 0.024 0.001 PHE A2158 TYR 0.019 0.001 TYR A1767 ARG 0.009 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 236 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7875 (t-100) REVERT: A 25 LEU cc_start: 0.8337 (tp) cc_final: 0.7745 (pt) REVERT: A 396 MET cc_start: 0.7090 (tmm) cc_final: 0.6821 (tmm) REVERT: A 728 VAL cc_start: 0.8855 (t) cc_final: 0.8508 (p) REVERT: A 1128 LEU cc_start: 0.8287 (tp) cc_final: 0.8070 (tt) REVERT: A 1558 MET cc_start: 0.8476 (tmm) cc_final: 0.7799 (tmm) REVERT: A 1679 GLU cc_start: 0.7790 (pt0) cc_final: 0.7434 (pt0) REVERT: A 2157 ASP cc_start: 0.7757 (m-30) cc_final: 0.7421 (m-30) outliers start: 41 outliers final: 24 residues processed: 265 average time/residue: 0.2165 time to fit residues: 91.4051 Evaluate side-chains 244 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 12 TRP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1858 VAL Chi-restraints excluded: chain A residue 2039 GLU Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.8980 chunk 157 optimal weight: 0.0010 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 0.0170 chunk 14 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14783 Z= 0.197 Angle : 0.701 14.460 20049 Z= 0.342 Chirality : 0.044 0.184 2277 Planarity : 0.004 0.064 2521 Dihedral : 4.485 24.091 1943 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 2.56 % Allowed : 20.01 % Favored : 77.43 % 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: -0.96 (0.20), residues: 1796 helix: 0.75 (0.16), residues: 1023 sheet: -1.52 (0.47), residues: 134 loop : -2.81 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 995 HIS 0.004 0.001 HIS A2006 PHE 0.021 0.001 PHE A2158 TYR 0.019 0.001 TYR A1767 ARG 0.004 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8366 (tp) cc_final: 0.7778 (pt) REVERT: A 396 MET cc_start: 0.7147 (tmm) cc_final: 0.6909 (tmm) REVERT: A 728 VAL cc_start: 0.8805 (t) cc_final: 0.8455 (p) REVERT: A 1128 LEU cc_start: 0.8272 (tp) cc_final: 0.8072 (tt) REVERT: A 1744 LEU cc_start: 0.8310 (tp) cc_final: 0.8023 (tt) REVERT: A 2157 ASP cc_start: 0.7783 (m-30) cc_final: 0.7413 (m-30) outliers start: 41 outliers final: 27 residues processed: 242 average time/residue: 0.2057 time to fit residues: 80.1205 Evaluate side-chains 241 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1853 LEU Chi-restraints excluded: chain A residue 1858 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.4980 chunk 19 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14783 Z= 0.191 Angle : 0.700 13.718 20049 Z= 0.339 Chirality : 0.044 0.201 2277 Planarity : 0.004 0.070 2521 Dihedral : 4.490 27.761 1943 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.24 % Allowed : 20.82 % Favored : 76.93 % 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: -0.98 (0.20), residues: 1796 helix: 0.74 (0.16), residues: 1023 sheet: -1.56 (0.46), residues: 134 loop : -2.81 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 995 HIS 0.004 0.001 HIS A2006 PHE 0.018 0.001 PHE A2158 TYR 0.019 0.001 TYR A1767 ARG 0.004 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 226 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8364 (tp) cc_final: 0.7775 (pt) REVERT: A 396 MET cc_start: 0.7073 (tmm) cc_final: 0.6818 (tmm) REVERT: A 644 MET cc_start: 0.7267 (ppp) cc_final: 0.6857 (ppp) REVERT: A 728 VAL cc_start: 0.8791 (t) cc_final: 0.8460 (p) REVERT: A 1128 LEU cc_start: 0.8291 (tp) cc_final: 0.8079 (tt) REVERT: A 1558 MET cc_start: 0.8513 (tmm) cc_final: 0.7946 (tmm) REVERT: A 1744 LEU cc_start: 0.8234 (tp) cc_final: 0.7818 (tt) REVERT: A 2157 ASP cc_start: 0.7807 (m-30) cc_final: 0.7537 (m-30) outliers start: 36 outliers final: 27 residues processed: 245 average time/residue: 0.2109 time to fit residues: 83.2043 Evaluate side-chains 244 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 217 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1853 LEU Chi-restraints excluded: chain A residue 1858 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 0.0970 chunk 118 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14783 Z= 0.181 Angle : 0.718 13.803 20049 Z= 0.347 Chirality : 0.044 0.219 2277 Planarity : 0.004 0.070 2521 Dihedral : 4.483 28.032 1943 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 2.00 % Allowed : 21.57 % Favored : 76.43 % 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: -0.97 (0.20), residues: 1796 helix: 0.75 (0.16), residues: 1022 sheet: -1.60 (0.46), residues: 135 loop : -2.80 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 995 HIS 0.004 0.001 HIS A2006 PHE 0.080 0.001 PHE A1222 TYR 0.019 0.001 TYR A1767 ARG 0.003 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8342 (tp) cc_final: 0.7756 (pt) REVERT: A 396 MET cc_start: 0.6942 (tmm) cc_final: 0.6651 (tmm) REVERT: A 644 MET cc_start: 0.7349 (ppp) cc_final: 0.7035 (ppp) REVERT: A 728 VAL cc_start: 0.8790 (t) cc_final: 0.8439 (p) REVERT: A 1128 LEU cc_start: 0.8278 (tp) cc_final: 0.8073 (tt) REVERT: A 1744 LEU cc_start: 0.8151 (tp) cc_final: 0.7920 (tt) REVERT: A 2157 ASP cc_start: 0.7789 (m-30) cc_final: 0.7522 (m-30) outliers start: 32 outliers final: 26 residues processed: 242 average time/residue: 0.2069 time to fit residues: 80.4529 Evaluate side-chains 243 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 153 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 GLN ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14783 Z= 0.224 Angle : 0.728 13.759 20049 Z= 0.356 Chirality : 0.044 0.222 2277 Planarity : 0.005 0.075 2521 Dihedral : 4.556 28.055 1943 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 2.49 % Allowed : 21.07 % Favored : 76.43 % 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: -0.99 (0.20), residues: 1796 helix: 0.70 (0.16), residues: 1027 sheet: -1.66 (0.46), residues: 134 loop : -2.76 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 995 HIS 0.005 0.001 HIS A2006 PHE 0.059 0.002 PHE A1222 TYR 0.023 0.002 TYR A 758 ARG 0.005 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 223 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8385 (tp) cc_final: 0.7783 (pt) REVERT: A 396 MET cc_start: 0.7007 (tmm) cc_final: 0.6716 (tmm) REVERT: A 644 MET cc_start: 0.7379 (ppp) cc_final: 0.7081 (ppp) REVERT: A 649 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7592 (tt) REVERT: A 1744 LEU cc_start: 0.8356 (tp) cc_final: 0.8086 (tt) REVERT: A 2157 ASP cc_start: 0.7863 (m-30) cc_final: 0.7556 (m-30) outliers start: 40 outliers final: 29 residues processed: 244 average time/residue: 0.2202 time to fit residues: 85.0246 Evaluate side-chains 246 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 995 TRP Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1398 ASP Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 119 optimal weight: 0.0370 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14783 Z= 0.188 Angle : 0.755 14.846 20049 Z= 0.361 Chirality : 0.045 0.237 2277 Planarity : 0.004 0.073 2521 Dihedral : 4.532 28.383 1943 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 2.06 % Allowed : 21.38 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.98 (0.20), residues: 1796 helix: 0.72 (0.16), residues: 1017 sheet: -1.61 (0.46), residues: 135 loop : -2.74 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 69 HIS 0.006 0.001 HIS A2006 PHE 0.034 0.001 PHE A1222 TYR 0.023 0.001 TYR A 758 ARG 0.010 0.000 ARG A2189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3592 Ramachandran restraints generated. 1796 Oldfield, 0 Emsley, 1796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8360 (tp) cc_final: 0.7764 (pt) REVERT: A 359 MET cc_start: 0.7390 (ptp) cc_final: 0.7151 (mtm) REVERT: A 396 MET cc_start: 0.6996 (tmm) cc_final: 0.6709 (tmm) REVERT: A 502 MET cc_start: 0.8258 (tmm) cc_final: 0.7955 (tmm) REVERT: A 644 MET cc_start: 0.7306 (ppp) cc_final: 0.6997 (ppp) REVERT: A 649 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7492 (tt) REVERT: A 1014 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: A 1744 LEU cc_start: 0.8333 (tp) cc_final: 0.8124 (tt) REVERT: A 2157 ASP cc_start: 0.7882 (m-30) cc_final: 0.7587 (m-30) outliers start: 33 outliers final: 28 residues processed: 245 average time/residue: 0.2094 time to fit residues: 82.3894 Evaluate side-chains 249 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 995 TRP Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1654 ASP Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1858 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 5.9990 chunk 132 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 143 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS ** A1774 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 = 0.3988 r_free = 0.3988 target = 0.111089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.094109 restraints weight = 52978.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096151 restraints weight = 33605.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.097578 restraints weight = 24204.209| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14783 Z= 0.185 Angle : 0.753 16.606 20049 Z= 0.359 Chirality : 0.044 0.240 2277 Planarity : 0.004 0.075 2521 Dihedral : 4.479 27.916 1943 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.24 % Allowed : 21.20 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.94 (0.20), residues: 1796 helix: 0.75 (0.16), residues: 1017 sheet: -1.51 (0.46), residues: 135 loop : -2.74 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 995 HIS 0.005 0.001 HIS A2006 PHE 0.024 0.001 PHE A1222 TYR 0.035 0.001 TYR A1710 ARG 0.010 0.000 ARG A2189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2766.04 seconds wall clock time: 51 minutes 23.90 seconds (3083.90 seconds total)