Starting phenix.real_space_refine on Thu Nov 16 09:40:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1h_14446/11_2023/7z1h_14446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1h_14446/11_2023/7z1h_14446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1h_14446/11_2023/7z1h_14446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1h_14446/11_2023/7z1h_14446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1h_14446/11_2023/7z1h_14446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1h_14446/11_2023/7z1h_14446.pdb" } resolution = 3.12 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= 0.039 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 99 5.16 5 C 9381 2.51 5 N 2590 2.21 5 O 2962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 772": "OE1" <-> "OE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1095": "OE1" <-> "OE2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1545": "OE1" <-> "OE2" Residue "A GLU 1711": "OE1" <-> "OE2" Residue "A TYR 1712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1915": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15032 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 15032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1848, 15032 Classifications: {'peptide': 1848} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 21, 'PCIS': 2, 'PTRANS': 48, 'TRANS': 1776} Chain breaks: 5 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: 7.47, per 1000 atoms: 0.50 Number of scatterers: 15032 At special positions: 0 Unit cell: (109.824, 143.936, 144.768, 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 99 16.00 O 2962 8.00 N 2590 7.00 C 9381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 6.03 Conformation dependent library (CDL) restraints added in 2.8 seconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 3 sheets defined 48.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 43 through 50 removed outlier: 3.646A pdb=" N LEU A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 54 removed outlier: 3.950A pdb=" N ILE A 54 " --> pdb=" O ILE A 51 " (cutoff:3.500A) No H-bonds generated for '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: 4.594A pdb=" N GLU A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 104' Processing helix chain 'A' and resid 120 through 141 removed outlier: 3.970A pdb=" N ALA A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 175 through 192 removed outlier: 4.443A pdb=" N LEU A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.625A pdb=" N ALA A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.730A pdb=" N VAL A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.909A pdb=" N ASP A 271 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 273 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.651A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.591A pdb=" N ILE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 287 " --> pdb=" O TRP A 283 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 366 through 375 removed outlier: 4.097A pdb=" N TYR A 369 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 575 Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 594 through 599 removed outlier: 4.496A pdb=" N CYS A 599 " --> pdb=" O GLU A 596 " (cutoff:3.500A) 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 684 Processing helix chain 'A' and resid 685 through 689 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 716 through 727 removed outlier: 4.020A pdb=" N ALA A 727 " --> pdb=" O MET A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 757 through 785 removed outlier: 4.569A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 816 removed outlier: 3.640A pdb=" N CYS A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 896 through 905 Processing helix chain 'A' and resid 907 through 911 removed outlier: 4.154A pdb=" N CYS A 910 " --> pdb=" O ASP A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 961 removed outlier: 3.643A pdb=" N LYS A 961 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.593A pdb=" N CYS A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1019 removed outlier: 4.170A pdb=" N ARG A1018 " --> pdb=" O THR A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1051 removed outlier: 4.218A pdb=" N THR A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1123 Processing helix chain 'A' and resid 1124 through 1132 removed outlier: 4.274A pdb=" N ASP A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1158 removed outlier: 3.544A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1166 removed outlier: 4.408A 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 1186 through 1197 removed outlier: 3.538A pdb=" N ILE A1190 " --> pdb=" O HIS A1186 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A1191 " --> pdb=" O GLY A1187 " (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 1292 through 1317 removed outlier: 4.021A pdb=" N LEU A1296 " --> pdb=" O THR A1292 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A1298 " --> pdb=" O GLU A1294 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A1299 " --> pdb=" O LEU A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1360 Processing helix chain 'A' and resid 1369 through 1374 removed outlier: 3.804A pdb=" N GLN A1373 " --> pdb=" O ILE A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1411 removed outlier: 4.105A pdb=" N GLU A1411 " --> pdb=" O ILE A1408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1408 through 1411' Processing helix chain 'A' and resid 1412 through 1424 removed outlier: 4.095A pdb=" N ASN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1478 Processing helix chain 'A' and resid 1501 through 1531 removed outlier: 4.156A pdb=" N LYS A1507 " --> pdb=" O ARG A1503 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A1508 " --> pdb=" O LYS A1504 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A1524 " --> pdb=" O ASP A1520 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A1525 " --> pdb=" O LYS A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1543 removed outlier: 5.057A pdb=" N GLU A1541 " --> pdb=" O ASP A1537 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 through 1549 removed outlier: 3.953A pdb=" N SER A1548 " --> pdb=" O GLU A1545 " (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 1569 No H-bonds generated for 'chain 'A' and resid 1567 through 1569' Processing helix chain 'A' and resid 1570 through 1575 Processing helix chain 'A' and resid 1625 through 1630 Processing helix chain 'A' and resid 1635 through 1643 removed outlier: 4.135A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1674 removed outlier: 3.565A pdb=" N GLU A1653 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1704 Processing helix chain 'A' and resid 1710 through 1724 removed outlier: 4.361A pdb=" N TYR A1715 " --> pdb=" O GLU A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1728 Processing helix chain 'A' and resid 1730 through 1744 Processing helix chain 'A' and resid 1755 through 1776 Processing helix chain 'A' and resid 1793 through 1821 Processing helix chain 'A' and resid 1836 through 1867 Proline residue: A1851 - end of helix removed outlier: 4.221A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1897 Processing helix chain 'A' and resid 1942 through 1947 removed outlier: 3.533A pdb=" N LEU A1947 " --> pdb=" O MET A1943 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1957 removed outlier: 4.138A pdb=" N HIS A1957 " --> pdb=" O LYS A1953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1985 removed outlier: 3.718A pdb=" N LEU A1985 " --> pdb=" O LYS A1981 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 568 through 570 Processing sheet with id=AA2, first strand: chain 'A' and resid 923 through 925 Processing sheet with id=AA3, first strand: chain 'A' and resid 1278 through 1279 removed outlier: 3.781A pdb=" N ARG A1285 " --> pdb=" O ASP A1279 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1638 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: 4.63 Time building geometry restraints manager: 6.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 5921 1.38 - 1.59: 9265 1.59 - 1.81: 85 1.81 - 2.02: 55 2.02 - 2.23: 4 Bond restraints: 15330 Sorted by residual: bond pdb=" CE2 PHE A 374 " pdb=" CZ PHE A 374 " ideal model delta sigma weight residual 1.382 2.227 -0.845 3.00e-02 1.11e+03 7.94e+02 bond pdb=" CD2 PHE A 374 " pdb=" CE2 PHE A 374 " ideal model delta sigma weight residual 1.382 2.225 -0.843 3.00e-02 1.11e+03 7.90e+02 bond pdb=" CE1 PHE A 374 " pdb=" CZ PHE A 374 " ideal model delta sigma weight residual 1.382 2.196 -0.814 3.00e-02 1.11e+03 7.37e+02 bond pdb=" CD1 PHE A 374 " pdb=" CE1 PHE A 374 " ideal model delta sigma weight residual 1.382 2.192 -0.810 3.00e-02 1.11e+03 7.29e+02 bond pdb=" CG PHE A 374 " pdb=" CD1 PHE A 374 " ideal model delta sigma weight residual 1.384 1.809 -0.425 2.10e-02 2.27e+03 4.09e+02 ... (remaining 15325 not shown) Histogram of bond angle deviations from ideal: 95.14 - 106.83: 302 106.83 - 118.52: 11643 118.52 - 130.21: 8581 130.21 - 141.90: 82 141.90 - 153.59: 4 Bond angle restraints: 20612 Sorted by residual: angle pdb=" C GLU A1381 " pdb=" N LYS A1382 " pdb=" CA LYS A1382 " ideal model delta sigma weight residual 122.42 150.76 -28.34 1.33e+00 5.65e-01 4.54e+02 angle pdb=" C ASN A 356 " pdb=" N LYS A 357 " pdb=" CA LYS A 357 " ideal model delta sigma weight residual 122.42 153.59 -31.17 1.55e+00 4.16e-01 4.04e+02 angle pdb=" C GLN A 343 " pdb=" N GLU A 344 " pdb=" CA GLU A 344 " ideal model delta sigma weight residual 121.71 147.78 -26.07 1.39e+00 5.18e-01 3.52e+02 angle pdb=" CA ASP A1375 " pdb=" C ASP A1375 " pdb=" N ILE A1376 " ideal model delta sigma weight residual 118.04 136.04 -18.00 1.32e+00 5.74e-01 1.86e+02 angle pdb=" C GLU A 341 " pdb=" N ASN A 342 " pdb=" CA ASN A 342 " ideal model delta sigma weight residual 121.54 146.49 -24.95 1.91e+00 2.74e-01 1.71e+02 ... (remaining 20607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8620 17.69 - 35.37: 632 35.37 - 53.06: 90 53.06 - 70.74: 16 70.74 - 88.43: 8 Dihedral angle restraints: 9366 sinusoidal: 3942 harmonic: 5424 Sorted by residual: dihedral pdb=" CA ILE A1380 " pdb=" C ILE A1380 " pdb=" N GLU A1381 " pdb=" CA GLU A1381 " ideal model delta harmonic sigma weight residual 180.00 117.07 62.93 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CA ILE A1376 " pdb=" C ILE A1376 " pdb=" N LYS A1377 " pdb=" CA LYS A1377 " ideal model delta harmonic sigma weight residual 180.00 121.70 58.30 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA THR A 338 " pdb=" C THR A 338 " pdb=" N GLU A 339 " pdb=" CA GLU A 339 " ideal model delta harmonic sigma weight residual 180.00 123.19 56.81 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 9363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1952 0.075 - 0.149: 154 0.149 - 0.224: 9 0.224 - 0.298: 3 0.298 - 0.373: 3 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CA LYS A 337 " pdb=" N LYS A 337 " pdb=" C LYS A 337 " pdb=" CB LYS A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ASP A1375 " pdb=" N ASP A1375 " pdb=" C ASP A1375 " pdb=" CB ASP A1375 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA GLU A1381 " pdb=" N GLU A1381 " pdb=" C GLU A1381 " pdb=" CB GLU A1381 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 2118 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 374 " -0.013 2.00e-02 2.50e+03 2.39e-02 9.98e+00 pdb=" CG PHE A 374 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 374 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 374 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 374 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 PHE A 374 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 374 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1375 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ASP A1375 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP A1375 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A1376 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 711 " -0.023 2.00e-02 2.50e+03 1.72e-02 7.41e+00 pdb=" CG TRP A 711 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 711 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 711 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 711 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 711 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 711 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 711 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 711 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 711 " 0.001 2.00e-02 2.50e+03 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 137 2.44 - 3.06: 10555 3.06 - 3.67: 22929 3.67 - 4.29: 32360 4.29 - 4.90: 52237 Nonbonded interactions: 118218 Sorted by model distance: nonbonded pdb=" O ASP A1375 " pdb=" N ILE A1379 " model vdw 1.830 2.520 nonbonded pdb=" N LYS A 357 " pdb=" CZ PHE A 374 " model vdw 1.905 3.420 nonbonded pdb=" O ASP A1375 " pdb=" N LYS A1382 " model vdw 1.920 2.520 nonbonded pdb=" N LYS A 357 " pdb=" CE2 PHE A 374 " model vdw 1.935 3.420 nonbonded pdb=" N LYS A1378 " pdb=" O GLU A1381 " model vdw 1.997 2.520 ... (remaining 118213 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: 4.020 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: 18.840 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 39.860 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.016 0.845 15330 Z= 0.935 Angle : 0.971 31.167 20612 Z= 0.597 Chirality : 0.045 0.373 2121 Planarity : 0.004 0.040 2679 Dihedral : 12.324 88.427 5882 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.84 % Favored : 88.67 % Rotamer: Outliers : 0.18 % Allowed : 0.84 % Favored : 98.98 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.31 (0.20), residues: 1836 helix: 1.42 (0.19), residues: 768 sheet: -1.10 (1.55), residues: 12 loop : -2.86 (0.17), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.875 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.2950 time to fit residues: 45.0022 Evaluate side-chains 68 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN A 965 GLN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 ASN ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1847 ASN ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.947 Angle : 0.925 30.832 20612 Z= 0.557 Chirality : 0.045 0.366 2121 Planarity : 0.004 0.050 2679 Dihedral : 5.780 62.825 2005 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.04 % Favored : 87.47 % Rotamer: Outliers : 0.72 % Allowed : 6.77 % Favored : 92.51 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.29 (0.20), residues: 1836 helix: 1.32 (0.19), residues: 802 sheet: -1.48 (1.52), residues: 12 loop : -2.87 (0.18), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 85 average time/residue: 0.2873 time to fit residues: 38.1226 Evaluate side-chains 73 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1604 time to fit residues: 4.5633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.936 Angle : 0.909 30.895 20612 Z= 0.549 Chirality : 0.044 0.348 2121 Planarity : 0.004 0.043 2679 Dihedral : 5.727 61.907 2005 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.06 % Favored : 88.45 % Rotamer: Outliers : 0.36 % Allowed : 9.22 % Favored : 90.42 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.25 (0.20), residues: 1836 helix: 1.39 (0.19), residues: 795 sheet: -1.38 (1.52), residues: 12 loop : -2.85 (0.18), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 80 average time/residue: 0.2754 time to fit residues: 35.2435 Evaluate side-chains 66 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1403 time to fit residues: 2.9040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 86 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 159 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 ASN ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.931 Angle : 0.903 30.905 20612 Z= 0.546 Chirality : 0.043 0.344 2121 Planarity : 0.003 0.041 2679 Dihedral : 5.651 61.764 2005 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.38 % Favored : 88.07 % Rotamer: Outliers : 0.96 % Allowed : 10.06 % Favored : 88.98 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.20 (0.20), residues: 1836 helix: 1.44 (0.19), residues: 801 sheet: -1.25 (1.56), residues: 12 loop : -2.85 (0.18), residues: 1023 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 84 average time/residue: 0.2782 time to fit residues: 37.2366 Evaluate side-chains 71 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1812 time to fit residues: 4.3924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 ASN ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.952 Angle : 0.917 30.931 20612 Z= 0.553 Chirality : 0.044 0.343 2121 Planarity : 0.004 0.054 2679 Dihedral : 5.736 64.819 2005 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.38 % Favored : 88.13 % Rotamer: Outliers : 1.02 % Allowed : 10.66 % Favored : 88.32 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.18 (0.20), residues: 1836 helix: 1.45 (0.19), residues: 801 sheet: -1.50 (1.45), residues: 12 loop : -2.84 (0.18), residues: 1023 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 87 average time/residue: 0.2723 time to fit residues: 37.4995 Evaluate side-chains 69 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1734 time to fit residues: 3.0326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.937 Angle : 0.906 30.929 20612 Z= 0.546 Chirality : 0.043 0.342 2121 Planarity : 0.004 0.063 2679 Dihedral : 5.701 64.810 2005 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.55 % Favored : 88.02 % Rotamer: Outliers : 0.96 % Allowed : 11.92 % Favored : 87.13 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.18 (0.20), residues: 1836 helix: 1.43 (0.19), residues: 804 sheet: -1.38 (1.49), residues: 12 loop : -2.83 (0.18), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 85 average time/residue: 0.2826 time to fit residues: 37.5388 Evaluate side-chains 73 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1493 time to fit residues: 4.2932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 177 optimal weight: 0.0010 chunk 110 optimal weight: 6.9990 chunk 108 optimal weight: 0.0570 chunk 81 optimal weight: 0.9990 overall best weight: 0.7308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 GLN ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.934 Angle : 0.911 30.916 20612 Z= 0.546 Chirality : 0.043 0.344 2121 Planarity : 0.004 0.105 2679 Dihedral : 5.679 64.978 2005 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.55 % Favored : 87.96 % Rotamer: Outliers : 0.30 % Allowed : 12.93 % Favored : 86.77 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.14 (0.20), residues: 1836 helix: 1.50 (0.19), residues: 802 sheet: -1.90 (1.58), residues: 12 loop : -2.84 (0.18), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 78 average time/residue: 0.2808 time to fit residues: 34.7230 Evaluate side-chains 70 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1386 time to fit residues: 3.0096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 30.0000 chunk 112 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 16 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.934 Angle : 0.907 30.922 20612 Z= 0.545 Chirality : 0.043 0.343 2121 Planarity : 0.004 0.101 2679 Dihedral : 5.641 65.636 2005 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.33 % Favored : 88.29 % Rotamer: Outliers : 0.30 % Allowed : 13.47 % Favored : 86.23 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.08 (0.20), residues: 1836 helix: 1.56 (0.19), residues: 798 sheet: -1.78 (1.60), residues: 12 loop : -2.80 (0.17), residues: 1026 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 1.696 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.2847 time to fit residues: 34.3686 Evaluate side-chains 71 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1372 time to fit residues: 3.2106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 99 optimal weight: 0.0370 chunk 71 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.836 15330 Z= 0.935 Angle : 0.916 30.917 20612 Z= 0.548 Chirality : 0.043 0.343 2121 Planarity : 0.004 0.099 2679 Dihedral : 5.632 65.807 2005 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.49 % Favored : 88.13 % Rotamer: Outliers : 0.18 % Allowed : 13.83 % Favored : 85.99 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: 1836 helix: 1.58 (0.19), residues: 799 sheet: -1.82 (1.57), residues: 12 loop : -2.81 (0.17), residues: 1025 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 74 average time/residue: 0.2731 time to fit residues: 32.6047 Evaluate side-chains 71 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1479 time to fit residues: 2.7073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 112 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 0.0040 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 GLN ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.837 15330 Z= 0.930 Angle : 0.909 30.915 20612 Z= 0.544 Chirality : 0.042 0.342 2121 Planarity : 0.004 0.099 2679 Dihedral : 5.592 65.930 2005 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.00 % Favored : 88.62 % Rotamer: Outliers : 0.00 % Allowed : 14.07 % Favored : 85.93 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: 1836 helix: 1.60 (0.19), residues: 802 sheet: -1.65 (1.62), residues: 12 loop : -2.84 (0.17), residues: 1022 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.720 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2720 time to fit residues: 30.3152 Evaluate side-chains 68 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 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 = 0.4477 r_free = 0.4477 target = 0.136434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.101443 restraints weight = 46834.769| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 4.52 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.837 15330 Z= 0.941 Angle : 0.917 30.921 20612 Z= 0.549 Chirality : 0.043 0.345 2121 Planarity : 0.004 0.099 2679 Dihedral : 5.604 65.532 2005 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.66 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 1.17 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.08 (0.20), residues: 1836 helix: 1.57 (0.19), residues: 810 sheet: -1.94 (1.53), residues: 12 loop : -2.86 (0.17), residues: 1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3013.44 seconds wall clock time: 56 minutes 57.31 seconds (3417.31 seconds total)