Starting phenix.real_space_refine (version: dev) on Mon Apr 4 22:50:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2022/6uz3_20951_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2022/6uz3_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_2022/6uz3_20951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2022/6uz3_20951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2022/6uz3_20951_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz3_20951/04_2022/6uz3_20951_updated.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 Convert atoms to be neutral 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9446 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1151, 9446 Unusual residues: {'9Z9': 5, 'BMA': 1, 'NAG': 8, '6OU': 11} Classifications: {'undetermined': 25, 'peptide': 1126} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 28, 'CIS': 1, 'TRANS': 1095, None: 25, 'PCIS': 1} Not linked: pdbres="ALA A1780 " pdbres="NAG A3001 " Not linked: pdbres="NAG A3001 " pdbres="NAG A3002 " Not linked: pdbres="NAG A3002 " pdbres="NAG A3003 " Not linked: pdbres="NAG A3003 " pdbres="NAG A3004 " Not linked: pdbres="NAG A3004 " pdbres="NAG A3005 " ... (remaining 20 not shown) Chain breaks: 7 Unresolved non-hydrogen bonds: 478 Unresolved non-hydrogen angles: 559 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, '6OU:plan-1': 9, '6OU:plan-2': 2, '6OU:plan-3': 1, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 120 Time building chain proxies: 6.21, per 1000 atoms: 0.66 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 A3001 " - " NAG A3002 " " NAG A3004 " - " NAG A3005 " " NAG A3005 " - " BMA A3006 " " NAG A3007 " - " NAG A3008 " NAG-ASN " NAG A3001 " - " ASN A1382 " " NAG A3003 " - " ASN A 319 " " NAG A3004 " - " ASN A 329 " " NAG A3007 " - " ASN A1390 " " NAG A3009 " - " ASN A 284 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 1.4 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... running ksdssp... Secondary structure from input PDB file: 52 helices and 1 sheets defined 70.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 150 Processing helix chain 'A' and resid 156 through 180 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 183 through 190 Processing helix chain 'A' and resid 193 through 210 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 222 through 233 removed outlier: 3.527A pdb=" N ARG A 226 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 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 252 through 272 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 305 through 314 Proline residue: A 312 - end of helix Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 388 through 423 removed outlier: 4.785A pdb=" N GLY A 401 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 403 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 404 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 405 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 406 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 416 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 717 removed outlier: 4.222A pdb=" N ASP A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 Processing helix chain 'A' and resid 744 through 771 removed outlier: 3.660A pdb=" N ILE A 770 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 Processing helix chain 'A' and resid 781 through 797 Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 816 through 822 Processing helix chain 'A' and resid 824 through 835 Processing helix chain 'A' and resid 841 through 857 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 859 through 866 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 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 888 through 899 Processing helix chain 'A' and resid 903 through 912 removed outlier: 4.502A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 943 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 1204 Processing helix chain 'A' and resid 1207 through 1226 Processing helix chain 'A' and resid 1231 through 1233 No H-bonds generated for 'chain 'A' and resid 1231 through 1233' Processing helix chain 'A' and resid 1235 through 1263 removed outlier: 3.509A pdb=" N VAL A1239 " --> pdb=" O LYS A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1270 Processing helix chain 'A' and resid 1272 through 1292 Processing helix chain 'A' and resid 1306 through 1318 Proline residue: A1312 - end of helix removed outlier: 3.942A pdb=" N LEU A1316 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1358 Proline residue: A1334 - end of helix 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 1387 through 1389 No H-bonds generated for 'chain 'A' and resid 1387 through 1389' Processing helix chain 'A' and resid 1408 through 1418 Processing helix chain 'A' and resid 1424 through 1431 Processing helix chain 'A' and resid 1446 through 1461 removed outlier: 3.903A pdb=" N VAL A1453 " --> pdb=" O ILE A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1481 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) Processing helix chain 'A' and resid 1491 through 1502 Processing helix chain 'A' and resid 1518 through 1527 Processing helix chain 'A' and resid 1530 through 1548 Processing helix chain 'A' and resid 1556 through 1581 Processing helix chain 'A' and resid 1587 through 1590 No H-bonds generated for 'chain 'A' and resid 1587 through 1590' Processing helix chain 'A' and resid 1592 through 1616 removed outlier: 3.879A pdb=" N ASP A1597 " --> pdb=" O TRP A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1627 Processing helix chain 'A' and resid 1630 through 1641 Processing helix chain 'A' and resid 1644 through 1680 removed outlier: 3.918A pdb=" N PHE A1650 " --> pdb=" O ARG A1646 " (cutoff:3.500A) Proline residue: A1657 - end of helix Processing helix chain 'A' and resid 1699 through 1711 removed outlier: 3.551A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1715 through 1723 Proline residue: A1721 - end of helix Processing helix chain 'A' and resid 1747 through 1779 Processing sheet with id= A, first strand: chain 'A' and resid 280 through 282 541 hydrogen bonds defined for protein. 1425 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: 2.85 Time building geometry restraints manager: 4.92 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: 5272 30.25 - 60.50: 256 60.50 - 90.74: 18 90.74 - 120.99: 5 120.99 - 151.24: 3 Dihedral angle restraints: 5554 sinusoidal: 2275 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 5551 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 A3002 " pdb=" O4 NAG A3001 " pdb=" C2 NAG A3002 " pdb=" O5 NAG A3002 " 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 A3006 " pdb=" O4 NAG A3005 " pdb=" C2 BMA A3006 " pdb=" O5 BMA A3006 " 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 A3007 " 0.361 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG A3007 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG A3007 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG A3007 " -0.550 2.00e-02 2.50e+03 pdb=" O7 NAG A3007 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3008 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG A3008 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A3008 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG A3008 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG A3008 " -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: 793 2.72 - 3.44: 14991 3.44 - 4.17: 21745 4.17 - 4.90: 38498 Nonbonded interactions: 76033 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 A3004 " model vdw 1.942 3.040 nonbonded pdb=" O CYS A 342 " pdb=" C7 NAG A3004 " model vdw 1.953 3.270 ... (remaining 76028 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 4.580 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 29.690 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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= 1.387 Angle : 1.319 20.455 13108 Z= 0.626 Chirality : 0.154 3.245 1547 Planarity : 0.015 0.310 1541 Dihedral : 17.520 151.241 3425 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 32.21 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 : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 264 average time/residue: 0.2079 time to fit residues: 78.5575 Evaluate side-chains 218 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 211 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1702 time to fit residues: 3.2068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 48 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.6944 ------------------------------------------------------------------------------- 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 A 865 ASN A 871 HIS ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN A1615 GLN ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 9670 Z= 0.300 Angle : 0.780 11.809 13108 Z= 0.391 Chirality : 0.049 0.672 1547 Planarity : 0.005 0.052 1541 Dihedral : 14.972 134.786 1467 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.84 % Favored : 91.89 % 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: -2.35 (0.24), residues: 1110 helix: -1.16 (0.17), residues: 779 sheet: -2.75 (1.38), residues: 10 loop : -2.15 (0.39), residues: 321 *********************** 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 260 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 1.120 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 248 average time/residue: 0.1909 time to fit residues: 67.9363 Evaluate side-chains 225 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1318 time to fit residues: 4.8796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 71 optimal weight: 0.0010 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- 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 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 9670 Z= 0.220 Angle : 0.711 12.078 13108 Z= 0.354 Chirality : 0.045 0.531 1547 Planarity : 0.005 0.096 1541 Dihedral : 13.771 126.342 1467 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer Outliers : 3.37 % 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: -1.55 (0.25), residues: 1110 helix: -0.48 (0.18), residues: 784 sheet: -2.83 (1.44), residues: 10 loop : -2.12 (0.39), residues: 316 *********************** 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 262 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 249 average time/residue: 0.1875 time to fit residues: 67.2543 Evaluate side-chains 231 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 214 time to evaluate : 1.112 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.1103 time to fit residues: 4.6281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 29 optimal weight: 0.0570 chunk 92 optimal weight: 6.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN A 827 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 ASN A1474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2662 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= 0.222 Angle : 0.711 12.701 13108 Z= 0.348 Chirality : 0.044 0.548 1547 Planarity : 0.004 0.069 1541 Dihedral : 13.170 121.957 1467 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.85 % Favored : 92.97 % Rotamer Outliers : 3.48 % 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: -1.16 (0.26), residues: 1110 helix: -0.20 (0.18), residues: 784 sheet: -3.02 (1.38), residues: 10 loop : -1.91 (0.39), residues: 316 *********************** 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 257 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 238 average time/residue: 0.1813 time to fit residues: 64.0224 Evaluate side-chains 225 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.064 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.0918 time to fit residues: 3.9417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** ** A1736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 9670 Z= 0.265 Angle : 0.745 13.212 13108 Z= 0.364 Chirality : 0.045 0.557 1547 Planarity : 0.005 0.097 1541 Dihedral : 12.873 119.676 1467 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.48 % Favored : 92.43 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % 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: -1.11 (0.26), residues: 1110 helix: -0.13 (0.18), residues: 788 sheet: -3.07 (1.33), residues: 10 loop : -2.00 (0.39), residues: 312 *********************** 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 238 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 230 average time/residue: 0.1779 time to fit residues: 60.8794 Evaluate side-chains 219 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 1.061 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.0961 time to fit residues: 3.1485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN A 827 ASN A 860 GLN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1736 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2909 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= 0.271 Angle : 0.739 13.092 13108 Z= 0.360 Chirality : 0.045 0.559 1547 Planarity : 0.005 0.069 1541 Dihedral : 12.581 116.623 1467 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.66 % Favored : 92.25 % Rotamer Outliers : 2.42 % 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: -0.95 (0.26), residues: 1110 helix: 0.03 (0.18), residues: 773 sheet: -3.12 (1.27), residues: 10 loop : -1.97 (0.38), residues: 327 *********************** 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 240 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 229 average time/residue: 0.1690 time to fit residues: 58.1612 Evaluate side-chains 220 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 1.022 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.0976 time to fit residues: 3.6523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3188 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= 0.200 Angle : 0.732 13.232 13108 Z= 0.352 Chirality : 0.044 0.508 1547 Planarity : 0.004 0.063 1541 Dihedral : 12.075 110.982 1467 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.21 % Favored : 92.70 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % 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: -0.77 (0.26), residues: 1110 helix: 0.17 (0.18), residues: 788 sheet: -3.06 (1.28), residues: 10 loop : -2.02 (0.39), residues: 312 *********************** 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 243 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 232 average time/residue: 0.1808 time to fit residues: 61.8432 Evaluate side-chains 226 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 0.956 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.0972 time to fit residues: 3.4574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.0170 chunk 96 optimal weight: 30.0000 overall best weight: 2.0022 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 9670 Z= 0.225 Angle : 0.742 13.991 13108 Z= 0.359 Chirality : 0.044 0.512 1547 Planarity : 0.005 0.115 1541 Dihedral : 11.802 106.589 1467 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % 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: -0.71 (0.26), residues: 1110 helix: 0.25 (0.18), residues: 787 sheet: -3.07 (1.27), residues: 10 loop : -2.12 (0.38), residues: 313 *********************** 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 232 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 226 average time/residue: 0.1814 time to fit residues: 60.6501 Evaluate side-chains 215 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 1.036 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0919 time to fit residues: 1.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 0.0070 chunk 62 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 9670 Z= 0.222 Angle : 0.755 14.757 13108 Z= 0.362 Chirality : 0.044 0.505 1547 Planarity : 0.005 0.096 1541 Dihedral : 11.558 103.413 1467 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.61 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % 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: -0.65 (0.26), residues: 1110 helix: 0.30 (0.19), residues: 775 sheet: -3.07 (1.27), residues: 10 loop : -1.99 (0.37), residues: 325 *********************** 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 228 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 221 average time/residue: 0.1833 time to fit residues: 59.4711 Evaluate side-chains 218 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 209 time to evaluate : 1.066 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1111 time to fit residues: 3.4112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.0470 chunk 114 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 72 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 9670 Z= 0.196 Angle : 0.763 15.594 13108 Z= 0.361 Chirality : 0.043 0.486 1547 Planarity : 0.004 0.088 1541 Dihedral : 11.081 103.306 1467 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.21 % Favored : 92.70 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % Twisted General : 0.09 % 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: -0.59 (0.26), residues: 1110 helix: 0.36 (0.19), residues: 775 sheet: -3.13 (1.23), residues: 10 loop : -2.04 (0.36), residues: 325 ********************** 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 231 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 227 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 228 average time/residue: 0.1910 time to fit residues: 63.9306 Evaluate side-chains 215 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 1.099 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0963 time to fit residues: 2.0731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 860 GLN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.175844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.143072 restraints weight = 17106.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.146920 restraints weight = 8618.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.149412 restraints weight = 5707.862| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 9670 Z= 0.290 Angle : 0.821 16.652 13108 Z= 0.391 Chirality : 0.047 0.533 1547 Planarity : 0.005 0.080 1541 Dihedral : 11.243 103.239 1467 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer Outliers : 1.05 % 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: -0.71 (0.26), residues: 1110 helix: 0.28 (0.18), residues: 773 sheet: -3.28 (1.17), residues: 10 loop : -2.08 (0.37), residues: 327 =============================================================================== Job complete usr+sys time: 1958.84 seconds wall clock time: 36 minutes 22.76 seconds (2182.76 seconds total)