Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 16:25:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/08_2023/7tdt_25838.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/08_2023/7tdt_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_25838/08_2023/7tdt_25838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/08_2023/7tdt_25838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/08_2023/7tdt_25838.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdt_25838/08_2023/7tdt_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 7.59, per 1000 atoms: 0.53 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: 6.08 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: 1.67 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: 8.59 Time building geometry restraints manager: 6.50 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: 1.180 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: 5.050 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 43.970 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.960 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2365 time to fit residues: 106.6507 Evaluate side-chains 221 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3438 ------------------------------------------------------------------------------- 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 ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN ** A1642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1462 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= 0.209 Angle : 0.693 9.041 20049 Z= 0.343 Chirality : 0.044 0.214 2277 Planarity : 0.005 0.077 2521 Dihedral : 4.457 24.454 1943 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer Outliers : 1.25 % 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: -0.69 (0.20), residues: 1796 helix: 0.98 (0.16), residues: 1030 sheet: -1.64 (0.44), residues: 138 loop : -2.69 (0.24), residues: 628 *********************** 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 265 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 245 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 252 average time/residue: 0.2324 time to fit residues: 91.9465 Evaluate side-chains 235 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 220 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1270 time to fit residues: 5.9535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.0010 chunk 51 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 146 optimal weight: 0.4980 chunk 163 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 132 optimal weight: 0.0060 overall best weight: 0.7006 ------------------------------------------------------------------------------- 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** ** A1610 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: 0.7184 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14783 Z= 0.182 Angle : 0.684 12.901 20049 Z= 0.332 Chirality : 0.043 0.189 2277 Planarity : 0.004 0.073 2521 Dihedral : 4.440 24.213 1943 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1796 helix: 0.87 (0.16), residues: 1023 sheet: -1.35 (0.47), residues: 123 loop : -2.75 (0.23), residues: 650 *********************** 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 260 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 249 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 254 average time/residue: 0.2362 time to fit residues: 94.0966 Evaluate side-chains 224 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 218 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1333 time to fit residues: 3.9062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 110 optimal weight: 5.9990 chunk 165 optimal weight: 0.0770 chunk 174 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- 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 ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7261 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14783 Z= 0.213 Angle : 0.685 12.302 20049 Z= 0.337 Chirality : 0.044 0.174 2277 Planarity : 0.004 0.066 2521 Dihedral : 4.476 24.770 1943 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer Outliers : 1.87 % 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: -0.90 (0.20), residues: 1796 helix: 0.78 (0.16), residues: 1024 sheet: -1.51 (0.47), residues: 133 loop : -2.74 (0.23), residues: 639 *********************** 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 257 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 245 average time/residue: 0.2157 time to fit residues: 84.7148 Evaluate side-chains 235 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1346 time to fit residues: 6.3718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2116 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= 0.172 Angle : 0.686 13.128 20049 Z= 0.331 Chirality : 0.043 0.178 2277 Planarity : 0.004 0.064 2521 Dihedral : 4.444 24.168 1943 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.16), residues: 1028 sheet: -1.51 (0.47), residues: 134 loop : -2.77 (0.23), residues: 634 *********************** 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 251 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 243 average time/residue: 0.2074 time to fit residues: 81.4269 Evaluate side-chains 223 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 215 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1315 time to fit residues: 4.1479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.9990 chunk 157 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- 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: 0.7250 moved from start: 0.2270 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= 0.193 Angle : 0.701 13.581 20049 Z= 0.339 Chirality : 0.044 0.187 2277 Planarity : 0.004 0.060 2521 Dihedral : 4.458 24.694 1943 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer Outliers : 1.25 % 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: 0.71 (0.16), residues: 1030 sheet: -1.49 (0.47), residues: 134 loop : -2.77 (0.23), residues: 632 *********************** 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 246 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 237 average time/residue: 0.2121 time to fit residues: 81.1938 Evaluate side-chains 218 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 210 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1327 time to fit residues: 4.3340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 8.9990 chunk 19 optimal weight: 0.0670 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 174 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- 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** A1610 ASN 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: 0.7241 moved from start: 0.2368 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= 0.184 Angle : 0.702 13.681 20049 Z= 0.337 Chirality : 0.043 0.205 2277 Planarity : 0.004 0.068 2521 Dihedral : 4.462 28.100 1943 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.16), residues: 1031 sheet: -1.49 (0.47), residues: 134 loop : -2.79 (0.23), residues: 631 *********************** 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 236 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 223 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 231 average time/residue: 0.2190 time to fit residues: 80.9664 Evaluate side-chains 218 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1298 time to fit residues: 3.3730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 118 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 0.0000 chunk 137 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2444 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= 0.179 Angle : 0.724 13.862 20049 Z= 0.345 Chirality : 0.044 0.219 2277 Planarity : 0.004 0.072 2521 Dihedral : 4.421 27.303 1943 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 1.12 % 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: 0.72 (0.16), residues: 1033 sheet: -1.53 (0.45), residues: 142 loop : -2.88 (0.23), residues: 621 *********************** 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 240 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 234 average time/residue: 0.2218 time to fit residues: 83.6925 Evaluate side-chains 226 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1357 time to fit residues: 4.9826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 162 optimal weight: 0.0770 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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: 0.7234 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 14783 Z= 0.195 Angle : 0.738 13.842 20049 Z= 0.352 Chirality : 0.044 0.227 2277 Planarity : 0.004 0.072 2521 Dihedral : 4.431 28.026 1943 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.16), residues: 1034 sheet: -1.50 (0.47), residues: 135 loop : -2.81 (0.23), residues: 627 *********************** 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 231 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 229 average time/residue: 0.2250 time to fit residues: 82.5822 Evaluate side-chains 218 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1386 time to fit residues: 3.3801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.0970 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 overall best weight: 2.4182 ------------------------------------------------------------------------------- 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: 0.7320 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 14783 Z= 0.256 Angle : 0.755 13.712 20049 Z= 0.368 Chirality : 0.045 0.224 2277 Planarity : 0.005 0.074 2521 Dihedral : 4.613 28.984 1943 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer Outliers : 0.62 % 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: -1.05 (0.20), residues: 1796 helix: 0.63 (0.16), residues: 1029 sheet: -1.65 (0.46), residues: 135 loop : -2.76 (0.23), residues: 632 ********************** 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 227 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 217 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 221 average time/residue: 0.2447 time to fit residues: 85.6935 Evaluate side-chains 216 residues out of total 1604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 1.842 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1679 time to fit residues: 4.3960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.0170 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 126 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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** ** A1774 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 = 0.3984 r_free = 0.3984 target = 0.110677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.093362 restraints weight = 53187.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.095498 restraints weight = 33549.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096946 restraints weight = 24064.167| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2666 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= 0.194 Angle : 0.777 15.297 20049 Z= 0.369 Chirality : 0.045 0.239 2277 Planarity : 0.004 0.074 2521 Dihedral : 4.545 27.745 1943 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer Outliers : 0.12 % 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: -1.07 (0.20), residues: 1796 helix: 0.62 (0.16), residues: 1027 sheet: -1.55 (0.46), residues: 135 loop : -2.79 (0.23), residues: 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.29 seconds wall clock time: 51 minutes 24.96 seconds (3084.96 seconds total)