Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 09:40:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2023/6uz3_20951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2023/6uz3_20951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2023/6uz3_20951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2023/6uz3_20951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2023/6uz3_20951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2023/6uz3_20951.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.024 sd= 0.849 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 67 5.16 5 C 6309 2.51 5 N 1424 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A GLU 1297": "OE1" <-> "OE2" Residue "A ARG 1305": "NH1" <-> "NH2" Residue "A ARG 1311": "NH1" <-> "NH2" Residue "A PHE 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1514": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9446 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8887 Classifications: {'peptide': 1126} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 1095} Chain breaks: 7 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 464 Unusual residues: {'6OU': 11, '9Z9': 5, 'NAG': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'6OU:plan-1': 9, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 5.46, per 1000 atoms: 0.58 Number of scatterers: 9446 At special positions: 0 Unit cell: (135.168, 125.664, 110.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 5 15.00 O 1641 8.00 N 1424 7.00 C 6309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.02 Simple disulfide: pdb=" SG CYS A1730 " - pdb=" SG CYS A1744 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A3003 " - " ASN A 319 " " NAG A3009 " - " ASN A 284 " " NAG B 1 " - " ASN A1382 " " NAG C 1 " - " ASN A 329 " " NAG D 1 " - " ASN A1390 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 78.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 151 removed outlier: 4.035A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 181 removed outlier: 3.671A pdb=" N LYS A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 192 through 211 removed outlier: 3.538A pdb=" N TRP A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 removed outlier: 3.527A pdb=" N ARG A 226 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.674A pdb=" N SER A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 removed outlier: 4.007A pdb=" N GLN A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 273 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.693A pdb=" N HIS A 279 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 312 through 315 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.822A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.766A pdb=" N LEU A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 720 through 737 Processing helix chain 'A' and resid 743 through 772 removed outlier: 3.660A pdb=" N ILE A 770 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 780 Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 806 through 810 removed outlier: 4.267A pdb=" N ARG A 809 " --> pdb=" O SER A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 823 removed outlier: 4.113A pdb=" N SER A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 836 Processing helix chain 'A' and resid 840 through 858 removed outlier: 3.607A pdb=" N VAL A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 removed outlier: 5.426A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 3.912A pdb=" N ILE A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 902 through 913 removed outlier: 4.502A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 944 removed outlier: 3.629A pdb=" N LEU A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1205 Processing helix chain 'A' and resid 1206 through 1226 Processing helix chain 'A' and resid 1230 through 1233 Processing helix chain 'A' and resid 1234 through 1264 removed outlier: 3.705A pdb=" N LYS A1238 " --> pdb=" O ARG A1234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1239 " --> pdb=" O LYS A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1271 removed outlier: 3.874A pdb=" N ASN A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1293 Processing helix chain 'A' and resid 1305 through 1313 removed outlier: 3.693A pdb=" N ARG A1308 " --> pdb=" O ARG A1305 " (cutoff:3.500A) Proline residue: A1312 - end of helix Processing helix chain 'A' and resid 1314 through 1319 removed outlier: 4.315A pdb=" N ARG A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1331 removed outlier: 3.804A pdb=" N VAL A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 4.666A pdb=" N ASN A1338 " --> pdb=" O PRO A1334 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A1339 " --> pdb=" O SER A1335 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A1350 " --> pdb=" O PHE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1390 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1423 through 1432 Processing helix chain 'A' and resid 1445 through 1447 No H-bonds generated for 'chain 'A' and resid 1445 through 1447' Processing helix chain 'A' and resid 1448 through 1462 removed outlier: 3.924A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1482 removed outlier: 3.517A pdb=" N ASP A1473 " --> pdb=" O GLY A1469 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A1480 " --> pdb=" O ASN A1476 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A1481 " --> pdb=" O GLN A1477 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A1482 " --> pdb=" O GLN A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1503 Processing helix chain 'A' and resid 1517 through 1528 Processing helix chain 'A' and resid 1529 through 1549 removed outlier: 4.279A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1582 Processing helix chain 'A' and resid 1586 through 1591 removed outlier: 4.272A pdb=" N ASN A1591 " --> pdb=" O TYR A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1617 removed outlier: 3.879A pdb=" N ASP A1597 " --> pdb=" O TRP A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1628 Processing helix chain 'A' and resid 1629 through 1636 Processing helix chain 'A' and resid 1637 through 1642 Processing helix chain 'A' and resid 1643 through 1655 removed outlier: 3.918A pdb=" N PHE A1650 " --> pdb=" O ARG A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1681 Processing helix chain 'A' and resid 1698 through 1711 removed outlier: 3.542A pdb=" N SER A1702 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 Proline residue: A1721 - end of helix removed outlier: 3.847A pdb=" N ASN A1724 " --> pdb=" O SER A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1780 removed outlier: 3.573A pdb=" N ALA A1780 " --> pdb=" O ASN A1776 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA2, first strand: chain 'A' and resid 1366 through 1367 599 hydrogen bonds defined for protein. 1737 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: 2.81 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1406 1.27 - 1.40: 2503 1.40 - 1.54: 5535 1.54 - 1.68: 102 1.68 - 1.81: 124 Bond restraints: 9670 Sorted by residual: bond pdb=" C06 9Z9 A3014 " pdb=" C07 9Z9 A3014 " ideal model delta sigma weight residual 1.520 1.131 0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" C06 9Z9 A3010 " pdb=" C07 9Z9 A3010 " ideal model delta sigma weight residual 1.520 1.137 0.383 2.00e-02 2.50e+03 3.67e+02 bond pdb=" C06 9Z9 A3011 " pdb=" C07 9Z9 A3011 " ideal model delta sigma weight residual 1.520 1.138 0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" C06 9Z9 A3012 " pdb=" C07 9Z9 A3012 " ideal model delta sigma weight residual 1.520 1.157 0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C06 9Z9 A3013 " pdb=" C07 9Z9 A3013 " ideal model delta sigma weight residual 1.520 1.160 0.360 2.00e-02 2.50e+03 3.23e+02 ... (remaining 9665 not shown) Histogram of bond angle deviations from ideal: 95.56 - 103.29: 111 103.29 - 111.02: 3915 111.02 - 118.75: 3891 118.75 - 126.48: 5061 126.48 - 134.21: 130 Bond angle restraints: 13108 Sorted by residual: angle pdb=" N LYS A1616 " pdb=" CA LYS A1616 " pdb=" C LYS A1616 " ideal model delta sigma weight residual 111.36 122.77 -11.41 1.09e+00 8.42e-01 1.09e+02 angle pdb=" N LYS A1302 " pdb=" CA LYS A1302 " pdb=" C LYS A1302 " ideal model delta sigma weight residual 113.18 102.85 10.33 1.21e+00 6.83e-01 7.28e+01 angle pdb=" N PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta sigma weight residual 103.25 111.59 -8.34 1.05e+00 9.07e-01 6.30e+01 angle pdb=" N THR A1622 " pdb=" CA THR A1622 " pdb=" CB THR A1622 " ideal model delta sigma weight residual 110.81 100.46 10.35 1.48e+00 4.57e-01 4.89e+01 angle pdb=" N THR A1622 " pdb=" CA THR A1622 " pdb=" C THR A1622 " ideal model delta sigma weight residual 114.04 105.84 8.20 1.24e+00 6.50e-01 4.37e+01 ... (remaining 13103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.25: 5219 30.25 - 60.50: 254 60.50 - 90.74: 16 90.74 - 120.99: 4 120.99 - 151.24: 3 Dihedral angle restraints: 5496 sinusoidal: 2217 harmonic: 3279 Sorted by residual: dihedral pdb=" CA ARG A1364 " pdb=" C ARG A1364 " pdb=" N CYS A1365 " pdb=" CA CYS A1365 " ideal model delta harmonic sigma weight residual -180.00 -126.13 -53.87 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" N PRO A1621 " pdb=" C PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta harmonic sigma weight residual 115.10 141.39 -26.29 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" C PRO A1621 " pdb=" N PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta harmonic sigma weight residual -120.70 -141.82 21.12 0 2.50e+00 1.60e-01 7.14e+01 ... (remaining 5493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.649: 1532 0.649 - 1.298: 9 1.298 - 1.947: 5 1.947 - 2.596: 0 2.596 - 3.245: 1 Chirality restraints: 1547 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.78 -1.62 2.00e-02 2.50e+03 6.56e+03 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-02 2.50e+03 3.98e+02 chirality pdb=" C1 NAG A3009 " pdb=" ND2 ASN A 284 " pdb=" C2 NAG A3009 " pdb=" O5 NAG A3009 " both_signs ideal model delta sigma weight residual False -2.40 0.84 -3.24 2.00e-01 2.50e+01 2.63e+02 ... (remaining 1544 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.361 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG D 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.550 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG D 2 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3009 " -0.260 2.00e-02 2.50e+03 2.23e-01 6.19e+02 pdb=" C7 NAG A3009 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A3009 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG A3009 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG A3009 " -0.195 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 6 1.99 - 2.72: 770 2.72 - 3.44: 14930 3.44 - 4.17: 21633 4.17 - 4.90: 38462 Nonbonded interactions: 75801 Sorted by model distance: nonbonded pdb=" O LEU A 129 " pdb=" CE2 PHE A 134 " model vdw 1.260 3.340 nonbonded pdb=" CD1 ILE A 138 " pdb=" OE2 GLU A 172 " model vdw 1.659 3.460 nonbonded pdb=" O LEU A 129 " pdb=" CZ PHE A 134 " model vdw 1.838 3.340 nonbonded pdb=" O CYS A 342 " pdb=" O7 NAG C 1 " model vdw 1.942 3.040 nonbonded pdb=" O CYS A 342 " pdb=" C7 NAG C 1 " model vdw 1.953 3.270 ... (remaining 75796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.510 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 : 0.022 0.389 9670 Z= 1.610 Angle : 1.330 20.455 13108 Z= 0.622 Chirality : 0.154 3.245 1547 Planarity : 0.015 0.310 1541 Dihedral : 17.373 151.241 3367 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 32.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.17 % Favored : 88.47 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % 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: -3.89 (0.22), residues: 1110 helix: -2.29 (0.15), residues: 783 sheet: -2.87 (1.28), residues: 10 loop : -2.83 (0.37), residues: 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 1.120 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 264 average time/residue: 0.1975 time to fit residues: 74.2362 Evaluate side-chains 218 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 211 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1356 time to fit residues: 2.7943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 314 ASN A 731 ASN A 739 HIS A 780 GLN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 ASN A 871 HIS ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1615 GLN ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9670 Z= 0.266 Angle : 0.811 12.088 13108 Z= 0.395 Chirality : 0.046 0.499 1547 Planarity : 0.005 0.049 1541 Dihedral : 14.085 133.424 1409 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.02 % Favored : 91.80 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.21 (0.24), residues: 1110 helix: -1.01 (0.17), residues: 790 sheet: -2.54 (1.45), residues: 10 loop : -2.27 (0.39), residues: 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 251 average time/residue: 0.1951 time to fit residues: 71.0964 Evaluate side-chains 224 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1257 time to fit residues: 4.1355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 731 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9670 Z= 0.204 Angle : 0.726 13.419 13108 Z= 0.354 Chirality : 0.043 0.389 1547 Planarity : 0.004 0.050 1541 Dihedral : 12.936 124.767 1409 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.39 % Favored : 92.43 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.17 (0.26), residues: 1110 helix: -0.23 (0.18), residues: 795 sheet: -2.88 (1.33), residues: 10 loop : -1.89 (0.41), residues: 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 1.064 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 243 average time/residue: 0.1930 time to fit residues: 68.8845 Evaluate side-chains 225 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 211 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1388 time to fit residues: 4.5823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 0.0970 chunk 53 optimal weight: 20.0000 chunk 96 optimal weight: 40.0000 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN A 860 GLN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9670 Z= 0.232 Angle : 0.724 12.820 13108 Z= 0.349 Chirality : 0.043 0.387 1547 Planarity : 0.004 0.047 1541 Dihedral : 12.224 120.547 1409 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.39 % Favored : 92.43 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.26), residues: 1110 helix: 0.08 (0.18), residues: 781 sheet: -3.05 (1.23), residues: 10 loop : -1.60 (0.41), residues: 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 217 time to evaluate : 0.932 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 233 average time/residue: 0.1783 time to fit residues: 61.1357 Evaluate side-chains 218 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0954 time to fit residues: 3.3929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9670 Z= 0.218 Angle : 0.731 13.072 13108 Z= 0.352 Chirality : 0.043 0.368 1547 Planarity : 0.004 0.043 1541 Dihedral : 11.732 119.259 1409 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 1110 helix: 0.24 (0.18), residues: 785 sheet: -3.02 (1.25), residues: 10 loop : -1.67 (0.40), residues: 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 1.032 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 236 average time/residue: 0.1903 time to fit residues: 65.9924 Evaluate side-chains 227 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1325 time to fit residues: 4.3694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 9670 Z= 0.304 Angle : 0.771 13.417 13108 Z= 0.376 Chirality : 0.045 0.406 1547 Planarity : 0.004 0.055 1541 Dihedral : 11.719 115.650 1409 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.84 % Favored : 91.98 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1110 helix: 0.14 (0.18), residues: 787 sheet: -3.22 (1.18), residues: 10 loop : -1.64 (0.41), residues: 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 0.961 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 233 average time/residue: 0.1762 time to fit residues: 60.9628 Evaluate side-chains 223 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0917 time to fit residues: 3.0183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN A1465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9670 Z= 0.184 Angle : 0.739 12.970 13108 Z= 0.355 Chirality : 0.042 0.328 1547 Planarity : 0.004 0.042 1541 Dihedral : 10.911 108.311 1409 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.30 % Favored : 92.52 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1110 helix: 0.38 (0.18), residues: 799 sheet: -3.03 (1.24), residues: 10 loop : -1.70 (0.39), residues: 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 234 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 237 average time/residue: 0.1938 time to fit residues: 67.8556 Evaluate side-chains 221 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1008 time to fit residues: 2.5862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0060 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 0.0370 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 103 optimal weight: 7.9990 overall best weight: 1.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS A1736 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 9670 Z= 0.198 Angle : 0.753 14.573 13108 Z= 0.362 Chirality : 0.043 0.332 1547 Planarity : 0.004 0.041 1541 Dihedral : 10.493 100.981 1409 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.76 % Favored : 93.06 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1110 helix: 0.47 (0.18), residues: 794 sheet: -3.17 (1.17), residues: 10 loop : -1.70 (0.38), residues: 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 223 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 226 average time/residue: 0.1796 time to fit residues: 60.8191 Evaluate side-chains 222 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 216 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0965 time to fit residues: 2.5659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN A1327 ASN ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 9670 Z= 0.205 Angle : 0.761 14.978 13108 Z= 0.363 Chirality : 0.043 0.325 1547 Planarity : 0.004 0.042 1541 Dihedral : 10.215 94.247 1409 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.12 % Favored : 92.70 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1110 helix: 0.53 (0.18), residues: 795 sheet: -3.24 (1.14), residues: 10 loop : -1.76 (0.38), residues: 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 218 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 221 average time/residue: 0.1834 time to fit residues: 60.0821 Evaluate side-chains 218 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 213 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1041 time to fit residues: 2.3901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.0970 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 9670 Z= 0.190 Angle : 0.759 15.787 13108 Z= 0.361 Chirality : 0.043 0.311 1547 Planarity : 0.004 0.040 1541 Dihedral : 9.831 84.042 1409 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.67 % Favored : 93.15 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1110 helix: 0.65 (0.18), residues: 783 sheet: -3.22 (1.10), residues: 10 loop : -1.60 (0.37), residues: 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 225 average time/residue: 0.1838 time to fit residues: 62.1555 Evaluate side-chains 216 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0996 time to fit residues: 1.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.180124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.147610 restraints weight = 16852.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.151586 restraints weight = 8366.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.154135 restraints weight = 5517.897| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 9670 Z= 0.205 Angle : 0.788 15.676 13108 Z= 0.374 Chirality : 0.044 0.404 1547 Planarity : 0.004 0.040 1541 Dihedral : 9.696 75.639 1409 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.76 % Favored : 93.06 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1110 helix: 0.60 (0.18), residues: 784 sheet: -3.26 (1.12), residues: 10 loop : -1.59 (0.37), residues: 316 =============================================================================== Job complete usr+sys time: 1954.94 seconds wall clock time: 36 minutes 17.41 seconds (2177.41 seconds total)