Starting phenix.real_space_refine on Mon Dec 11 15:22:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z12_14438/12_2023/7z12_14438.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z12_14438/12_2023/7z12_14438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z12_14438/12_2023/7z12_14438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z12_14438/12_2023/7z12_14438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z12_14438/12_2023/7z12_14438.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z12_14438/12_2023/7z12_14438.pdb" } resolution = 3.0 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= 0.043 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 110 5.16 5 C 11465 2.51 5 N 3159 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 49": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A ASP 698": "OD1" <-> "OD2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1188": "OE1" <-> "OE2" Residue "A PHE 1461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1520": "OD1" <-> "OD2" Residue "A ASP 1537": "OD1" <-> "OD2" Residue "A PHE 1551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1711": "OE1" <-> "OE2" Residue "A PHE 1806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1845": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18352 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1650 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} Chain: "C" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "A" Number of atoms: 15071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1853, 15071 Classifications: {'peptide': 1853} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 20, 'PCIS': 2, 'PTRANS': 48, 'TRANS': 1782} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 9.82, per 1000 atoms: 0.54 Number of scatterers: 18352 At special positions: 0 Unit cell: (111.488, 156.416, 159.744, 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 110 16.00 O 3618 8.00 N 3159 7.00 C 11465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 107 " distance=2.02 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 213 " distance=2.04 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: 7.10 Conformation dependent library (CDL) restraints added in 3.5 seconds 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4292 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 16 sheets defined 39.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.932A pdb=" N VAL C 102 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 51 through 54 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.543A pdb=" N GLU A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 4.246A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 removed outlier: 4.401A pdb=" N ALA A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 206 through 218 removed outlier: 4.063A pdb=" N ALA A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.995A pdb=" N VAL A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.918A pdb=" N LEU A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.820A pdb=" N LYS A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 366 through 378 removed outlier: 3.795A pdb=" N VAL A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 641 through 661 Processing helix chain 'A' and resid 672 through 687 removed outlier: 4.762A pdb=" N PHE A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 715 through 728 removed outlier: 3.511A pdb=" N ILE A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 removed outlier: 4.250A pdb=" N ASP A 754 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 786 removed outlier: 4.127A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 786 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 816 removed outlier: 3.825A pdb=" N GLU A 806 " --> pdb=" O LYS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 851 removed outlier: 3.534A pdb=" N LYS A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 896 through 905 Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 974 through 979 Processing helix chain 'A' and resid 1025 through 1049 removed outlier: 4.149A pdb=" N THR A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1125 removed outlier: 3.717A pdb=" N ASP A1109 " --> pdb=" O GLU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 Processing helix chain 'A' and resid 1140 through 1157 removed outlier: 3.930A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1166 removed outlier: 3.845A pdb=" N ILE A1165 " --> pdb=" O TRP A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1181 Processing helix chain 'A' and resid 1188 through 1197 removed outlier: 4.243A pdb=" N LYS A1194 " --> pdb=" O ILE A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'A' and resid 1294 through 1302 Processing helix chain 'A' and resid 1308 through 1313 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1349 through 1360 Processing helix chain 'A' and resid 1368 through 1380 removed outlier: 3.938A pdb=" N LEU A1372 " --> pdb=" O HIS A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1426 Processing helix chain 'A' and resid 1448 through 1477 removed outlier: 4.131A pdb=" N PHE A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1530 removed outlier: 4.573A pdb=" N LYS A1507 " --> pdb=" O ARG A1503 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A1508 " --> pdb=" O LYS A1504 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A1524 " --> pdb=" O ASP A1520 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A1525 " --> pdb=" O LYS A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1541 removed outlier: 4.396A pdb=" N GLU A1541 " --> pdb=" O ASP A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1543 through 1547 removed outlier: 3.715A pdb=" N ILE A1547 " --> pdb=" O PRO A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1555 Processing helix chain 'A' and resid 1558 through 1565 Processing helix chain 'A' and resid 1567 through 1574 removed outlier: 4.529A pdb=" N SER A1572 " --> pdb=" O ASP A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1630 Processing helix chain 'A' and resid 1635 through 1643 removed outlier: 3.877A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1674 removed outlier: 3.559A pdb=" N GLU A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1703 Processing helix chain 'A' and resid 1712 through 1725 Processing helix chain 'A' and resid 1730 through 1743 Processing helix chain 'A' and resid 1755 through 1776 Processing helix chain 'A' and resid 1793 through 1821 Processing helix chain 'A' and resid 1827 through 1831 Processing helix chain 'A' and resid 1837 through 1867 Proline residue: A1851 - end of helix removed outlier: 3.788A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A1865 " --> pdb=" O ASN A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1896 Processing helix chain 'A' and resid 1923 through 1927 removed outlier: 4.054A pdb=" N LEU A1926 " --> pdb=" O ASN A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1948 removed outlier: 3.661A pdb=" N GLU A1945 " --> pdb=" O ASP A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1956 Processing helix chain 'A' and resid 1957 through 1985 removed outlier: 3.912A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A1981 " --> pdb=" O ASP A1977 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 79 removed outlier: 5.222A pdb=" N TRP B 66 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 131 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79 removed outlier: 5.222A pdb=" N TRP B 66 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.866A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 169 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 210 " --> pdb=" O HIS B 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.866A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 169 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 183 removed outlier: 3.612A pdb=" N THR B 180 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR B 223 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 23 through 26 removed outlier: 4.407A pdb=" N PHE C 90 " --> pdb=" O CYS C 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 32 Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 73 removed outlier: 6.497A pdb=" N TRP C 54 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR C 68 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 52 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 73 removed outlier: 6.497A pdb=" N TRP C 54 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR C 68 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 52 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 151 through 158 removed outlier: 4.673A pdb=" N TYR C 192 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 163 through 169 Processing sheet with id=AB4, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AB5, first strand: chain 'A' and resid 569 through 570 Processing sheet with id=AB6, first strand: chain 'A' and resid 854 through 856 removed outlier: 7.711A pdb=" N ALA A 855 " --> pdb=" O SER A 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 923 through 925 708 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.93 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3688 1.33 - 1.45: 4515 1.45 - 1.57: 10385 1.57 - 1.69: 1 1.69 - 1.81: 134 Bond restraints: 18723 Sorted by residual: bond pdb=" CA SER A 564 " pdb=" CB SER A 564 " ideal model delta sigma weight residual 1.530 1.456 0.074 1.69e-02 3.50e+03 1.91e+01 bond pdb=" C TYR A 632 " pdb=" N PRO A 633 " ideal model delta sigma weight residual 1.335 1.368 -0.033 8.70e-03 1.32e+04 1.42e+01 bond pdb=" CA LYS A1203 " pdb=" C LYS A1203 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.40e+01 bond pdb=" CA SER A 700 " pdb=" CB SER A 700 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.55e-02 4.16e+03 1.21e+01 bond pdb=" CA SER A 703 " pdb=" CB SER A 703 " ideal model delta sigma weight residual 1.531 1.477 0.055 1.58e-02 4.01e+03 1.19e+01 ... (remaining 18718 not shown) Histogram of bond angle deviations from ideal: 95.99 - 103.62: 168 103.62 - 111.25: 7117 111.25 - 118.87: 7947 118.87 - 126.50: 9691 126.50 - 134.13: 305 Bond angle restraints: 25228 Sorted by residual: angle pdb=" N LYS A1203 " pdb=" CA LYS A1203 " pdb=" C LYS A1203 " ideal model delta sigma weight residual 110.80 127.59 -16.79 2.13e+00 2.20e-01 6.21e+01 angle pdb=" C LYS A 562 " pdb=" CA LYS A 562 " pdb=" CB LYS A 562 " ideal model delta sigma weight residual 110.42 95.99 14.43 1.99e+00 2.53e-01 5.26e+01 angle pdb=" C THR A 694 " pdb=" CA THR A 694 " pdb=" CB THR A 694 " ideal model delta sigma weight residual 115.89 106.54 9.35 1.32e+00 5.74e-01 5.01e+01 angle pdb=" N ILE A 7 " pdb=" CA ILE A 7 " pdb=" C ILE A 7 " ideal model delta sigma weight residual 113.20 106.56 6.64 9.60e-01 1.09e+00 4.78e+01 angle pdb=" C TYR A 701 " pdb=" CA TYR A 701 " pdb=" CB TYR A 701 " ideal model delta sigma weight residual 109.84 119.97 -10.13 1.50e+00 4.44e-01 4.56e+01 ... (remaining 25223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.57: 10771 25.57 - 51.13: 553 51.13 - 76.70: 61 76.70 - 102.26: 18 102.26 - 127.83: 1 Dihedral angle restraints: 11404 sinusoidal: 4716 harmonic: 6688 Sorted by residual: dihedral pdb=" CA CYS A1202 " pdb=" C CYS A1202 " pdb=" N LYS A1203 " pdb=" CA LYS A1203 " ideal model delta harmonic sigma weight residual 180.00 52.17 127.83 0 5.00e+00 4.00e-02 6.54e+02 dihedral pdb=" CA ASP A 698 " pdb=" C ASP A 698 " pdb=" N THR A 699 " pdb=" CA THR A 699 " ideal model delta harmonic sigma weight residual 180.00 93.79 86.21 0 5.00e+00 4.00e-02 2.97e+02 dihedral pdb=" CA LEU A 236 " pdb=" C LEU A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta harmonic sigma weight residual 180.00 -120.77 -59.23 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 11401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2236 0.074 - 0.148: 356 0.148 - 0.221: 43 0.221 - 0.295: 4 0.295 - 0.369: 5 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CB ILE A 118 " pdb=" CA ILE A 118 " pdb=" CG1 ILE A 118 " pdb=" CG2 ILE A 118 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA LYS A1203 " pdb=" N LYS A1203 " pdb=" C LYS A1203 " pdb=" CB LYS A1203 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB VAL A 945 " pdb=" CA VAL A 945 " pdb=" CG1 VAL A 945 " pdb=" CG2 VAL A 945 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2641 not shown) Planarity restraints: 3273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 632 " 0.099 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO A 633 " -0.261 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 951 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO A 952 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 952 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 952 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1822 " -0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A1823 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A1823 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1823 " -0.052 5.00e-02 4.00e+02 ... (remaining 3270 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.67: 3 1.67 - 2.48: 215 2.48 - 3.29: 23048 3.29 - 4.09: 48917 4.09 - 4.90: 86547 Warning: very small nonbonded interaction distances. Nonbonded interactions: 158730 Sorted by model distance: nonbonded pdb=" NZ LYS A 690 " pdb=" CE LYS A 691 " model vdw 0.865 3.520 nonbonded pdb=" NZ LYS A 690 " pdb=" CD LYS A 691 " model vdw 1.321 3.520 nonbonded pdb=" CE LYS A 690 " pdb=" CE LYS A 691 " model vdw 1.539 3.840 nonbonded pdb=" NZ LYS A 690 " pdb=" NZ LYS A 691 " model vdw 1.982 3.200 nonbonded pdb=" OG1 THR A 872 " pdb=" O GLU A 874 " model vdw 2.019 2.440 ... (remaining 158725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 0.020 Extract box with map and model: 18.320 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 50.300 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 18723 Z= 0.432 Angle : 1.033 16.790 25228 Z= 0.609 Chirality : 0.056 0.369 2644 Planarity : 0.006 0.151 3273 Dihedral : 15.278 127.830 7100 Min Nonbonded Distance : 0.865 Molprobity Statistics. All-atom Clashscore : 31.24 Ramachandran Plot: Outliers : 1.14 % Allowed : 14.96 % Favored : 83.89 % Rotamer: Outliers : 1.37 % Allowed : 1.08 % Favored : 97.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 2.78 % Twisted General : 1.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.16), residues: 2272 helix: -0.96 (0.17), residues: 835 sheet: -0.49 (0.37), residues: 208 loop : -3.22 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 223 HIS 0.010 0.002 HIS A 888 PHE 0.039 0.003 PHE B 46 TYR 0.045 0.002 TYR A 701 ARG 0.012 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 7 residues processed: 183 average time/residue: 1.3720 time to fit residues: 283.3861 Evaluate side-chains 125 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 2.034 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 2.9451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN A 528 GLN A 867 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1167 ASN ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 GLN A1659 GLN A1674 ASN ** A1861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 18723 Z= 0.247 Angle : 0.831 10.430 25228 Z= 0.448 Chirality : 0.048 0.376 2644 Planarity : 0.005 0.100 3273 Dihedral : 8.680 58.425 2478 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.26 % Favored : 85.30 % Rotamer: Outliers : 1.67 % Allowed : 8.48 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.17), residues: 2272 helix: -0.53 (0.18), residues: 829 sheet: -0.26 (0.37), residues: 212 loop : -3.10 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 223 HIS 0.009 0.001 HIS A 888 PHE 0.021 0.002 PHE A1031 TYR 0.031 0.002 TYR A1314 ARG 0.006 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 2.271 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 9 residues processed: 163 average time/residue: 1.4715 time to fit residues: 270.3924 Evaluate side-chains 122 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 2.217 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.3232 time to fit residues: 4.4865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN C 229 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN A1008 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 ASN ** A1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 GLN A1749 ASN ** A1861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18723 Z= 0.321 Angle : 0.811 10.743 25228 Z= 0.437 Chirality : 0.048 0.307 2644 Planarity : 0.005 0.101 3273 Dihedral : 8.233 57.092 2478 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.52 % Favored : 85.08 % Rotamer: Outliers : 1.91 % Allowed : 13.00 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.95 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.17), residues: 2272 helix: -0.28 (0.18), residues: 821 sheet: -0.25 (0.37), residues: 214 loop : -3.06 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 283 HIS 0.010 0.002 HIS A1957 PHE 0.027 0.002 PHE A1121 TYR 0.024 0.002 TYR A1314 ARG 0.007 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 2.078 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 157 average time/residue: 1.2355 time to fit residues: 223.1763 Evaluate side-chains 130 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 4 average time/residue: 0.2895 time to fit residues: 4.8846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 197 optimal weight: 0.0070 chunk 59 optimal weight: 0.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 ASN ** A1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 GLN ** A1861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18723 Z= 0.211 Angle : 0.759 11.236 25228 Z= 0.407 Chirality : 0.046 0.314 2644 Planarity : 0.005 0.089 3273 Dihedral : 7.858 55.912 2478 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.29 % Favored : 86.36 % Rotamer: Outliers : 2.65 % Allowed : 14.37 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.86 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2272 helix: -0.19 (0.18), residues: 839 sheet: -0.18 (0.37), residues: 214 loop : -2.89 (0.16), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 223 HIS 0.007 0.001 HIS A1345 PHE 0.028 0.002 PHE A1343 TYR 0.021 0.002 TYR A1314 ARG 0.009 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 129 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 21 residues processed: 175 average time/residue: 1.1807 time to fit residues: 239.2702 Evaluate side-chains 131 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 2.153 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 7 average time/residue: 0.4654 time to fit residues: 7.4389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 0.3980 chunk 152 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN A 261 HIS ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN A 524 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18723 Z= 0.329 Angle : 0.787 10.462 25228 Z= 0.421 Chirality : 0.047 0.267 2644 Planarity : 0.005 0.094 3273 Dihedral : 7.694 53.555 2478 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.35 % Favored : 85.39 % Rotamer: Outliers : 2.21 % Allowed : 16.87 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.17), residues: 2272 helix: -0.10 (0.18), residues: 830 sheet: -0.14 (0.37), residues: 214 loop : -2.86 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 223 HIS 0.007 0.001 HIS A1957 PHE 0.020 0.002 PHE A1031 TYR 0.021 0.002 TYR A 923 ARG 0.009 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 25 residues processed: 154 average time/residue: 1.1728 time to fit residues: 209.4575 Evaluate side-chains 138 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 2.166 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 7 average time/residue: 0.3398 time to fit residues: 6.4841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 50.0000 chunk 198 optimal weight: 0.6980 chunk 43 optimal weight: 0.0670 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 183 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18723 Z= 0.195 Angle : 0.742 13.205 25228 Z= 0.396 Chirality : 0.046 0.283 2644 Planarity : 0.005 0.085 3273 Dihedral : 7.498 52.647 2478 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.63 % Favored : 87.10 % Rotamer: Outliers : 2.75 % Allowed : 17.75 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 2272 helix: 0.06 (0.19), residues: 824 sheet: -0.02 (0.37), residues: 214 loop : -2.72 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 223 HIS 0.013 0.001 HIS A1957 PHE 0.019 0.002 PHE A1121 TYR 0.022 0.002 TYR A1044 ARG 0.010 0.001 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 126 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 21 residues processed: 173 average time/residue: 1.2304 time to fit residues: 244.2439 Evaluate side-chains 132 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 3 average time/residue: 0.6808 time to fit residues: 5.5645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 233 ASN A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18723 Z= 0.311 Angle : 0.784 11.717 25228 Z= 0.417 Chirality : 0.047 0.334 2644 Planarity : 0.005 0.088 3273 Dihedral : 7.464 54.040 2478 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.07 % Favored : 86.62 % Rotamer: Outliers : 2.21 % Allowed : 18.88 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2272 helix: 0.05 (0.19), residues: 830 sheet: -0.03 (0.37), residues: 214 loop : -2.74 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 223 HIS 0.008 0.001 HIS A1957 PHE 0.045 0.002 PHE A1343 TYR 0.021 0.002 TYR A 701 ARG 0.011 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 23 residues processed: 162 average time/residue: 1.1255 time to fit residues: 211.7034 Evaluate side-chains 137 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 2 average time/residue: 0.7457 time to fit residues: 4.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.0670 chunk 42 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 149 optimal weight: 0.0670 chunk 108 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18723 Z= 0.198 Angle : 0.765 11.530 25228 Z= 0.403 Chirality : 0.046 0.358 2644 Planarity : 0.005 0.086 3273 Dihedral : 7.327 56.896 2478 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.68 % Favored : 87.06 % Rotamer: Outliers : 2.01 % Allowed : 19.57 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.50 % 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: -1.85 (0.18), residues: 2272 helix: 0.21 (0.19), residues: 825 sheet: 0.06 (0.37), residues: 213 loop : -2.63 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 223 HIS 0.007 0.001 HIS A1957 PHE 0.024 0.002 PHE A1343 TYR 0.030 0.001 TYR A1044 ARG 0.011 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 126 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 159 average time/residue: 1.1179 time to fit residues: 206.1994 Evaluate side-chains 135 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.939 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 0.6606 time to fit residues: 5.5320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 233 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN A 852 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 GLN ** A1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18723 Z= 0.239 Angle : 0.778 12.990 25228 Z= 0.408 Chirality : 0.046 0.381 2644 Planarity : 0.005 0.083 3273 Dihedral : 7.229 54.944 2478 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.94 % Favored : 86.84 % Rotamer: Outliers : 1.86 % Allowed : 20.16 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.50 % 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: -1.84 (0.18), residues: 2272 helix: 0.24 (0.19), residues: 829 sheet: 0.07 (0.38), residues: 213 loop : -2.66 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 223 HIS 0.009 0.001 HIS A1957 PHE 0.025 0.002 PHE A1343 TYR 0.025 0.001 TYR A1314 ARG 0.012 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 148 average time/residue: 1.1774 time to fit residues: 203.2785 Evaluate side-chains 134 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 3.1668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 0.0770 chunk 150 optimal weight: 0.0050 chunk 227 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 233 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 GLN ** A1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18723 Z= 0.200 Angle : 0.768 12.785 25228 Z= 0.401 Chirality : 0.046 0.413 2644 Planarity : 0.005 0.091 3273 Dihedral : 7.098 53.741 2478 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.24 % Favored : 87.59 % Rotamer: Outliers : 1.42 % Allowed : 20.30 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.45 % 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: -1.74 (0.18), residues: 2272 helix: 0.35 (0.19), residues: 820 sheet: 0.13 (0.38), residues: 213 loop : -2.59 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 223 HIS 0.009 0.001 HIS A1957 PHE 0.019 0.002 PHE A1343 TYR 0.026 0.001 TYR A1044 ARG 0.012 0.001 ARG C 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 149 average time/residue: 1.1576 time to fit residues: 199.9205 Evaluate side-chains 132 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 2.091 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 1 average time/residue: 0.3282 time to fit residues: 3.4648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 159 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: B 226 ASN B 233 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.131717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088075 restraints weight = 50469.318| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.99 r_work: 0.3168 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18723 Z= 0.266 Angle : 0.778 11.831 25228 Z= 0.409 Chirality : 0.047 0.418 2644 Planarity : 0.005 0.084 3273 Dihedral : 7.056 56.028 2478 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.76 % Favored : 87.06 % Rotamer: Outliers : 1.37 % Allowed : 20.60 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.45 % 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: -1.76 (0.18), residues: 2272 helix: 0.31 (0.19), residues: 829 sheet: 0.23 (0.39), residues: 205 loop : -2.62 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 223 HIS 0.009 0.001 HIS A1957 PHE 0.023 0.002 PHE A1343 TYR 0.020 0.001 TYR B 79 ARG 0.010 0.001 ARG C 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5646.21 seconds wall clock time: 104 minutes 53.42 seconds (6293.42 seconds total)