Starting phenix.real_space_refine on Fri Mar 15 20:57:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kle_0709/03_2024/6kle_0709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kle_0709/03_2024/6kle_0709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kle_0709/03_2024/6kle_0709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kle_0709/03_2024/6kle_0709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kle_0709/03_2024/6kle_0709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kle_0709/03_2024/6kle_0709.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 1 6.06 5 P 7 5.49 5 S 84 5.16 5 C 8114 2.51 5 N 2148 2.21 5 O 2414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12769 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1592, 12618 Classifications: {'peptide': 1592} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 47, 'TRANS': 1544} Chain breaks: 16 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 284 38.187 73.702 27.629 1.00 99.80 S ATOM 2195 SG CYS A 287 41.806 72.573 27.328 1.00103.32 S ATOM 3474 SG CYS A 470 40.392 74.466 24.347 1.00121.98 S Time building chain proxies: 7.26, per 1000 atoms: 0.57 Number of scatterers: 12769 At special positions: 0 Unit cell: (112.88, 115.6, 121.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 1 24.99 S 84 16.00 P 7 15.00 O 2414 8.00 N 2148 7.00 C 8114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " Number of angles added : 3 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3034 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 9 sheets defined 54.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.808A pdb=" N GLY A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 56 removed outlier: 4.236A pdb=" N THR A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 68 through 76 removed outlier: 3.582A pdb=" N ILE A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 125 removed outlier: 3.897A pdb=" N ASN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.725A pdb=" N SER A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.630A pdb=" N LEU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 248 removed outlier: 3.925A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.708A pdb=" N CYS A 287 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.971A pdb=" N GLY A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 411 through 420 removed outlier: 4.410A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 503 removed outlier: 3.639A pdb=" N ARG A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.985A pdb=" N PHE A 579 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU A 580 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 609 through 623 Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.768A pdb=" N GLN A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 663 through 680 removed outlier: 3.947A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 removed outlier: 3.988A pdb=" N ARG A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 713 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.637A pdb=" N LEU A 780 " --> pdb=" O CYS A 776 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 Processing helix chain 'A' and resid 864 through 874 removed outlier: 3.917A pdb=" N LEU A 868 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 869 " --> pdb=" O THR A 865 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 921 removed outlier: 3.803A pdb=" N ASP A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 968 removed outlier: 3.786A pdb=" N VAL A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.777A pdb=" N VAL A 974 " --> pdb=" O ASP A 971 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 975 " --> pdb=" O PRO A 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 975' Processing helix chain 'A' and resid 981 through 990 removed outlier: 3.518A pdb=" N LYS A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1024 through 1035 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1191 through 1196 removed outlier: 3.593A pdb=" N THR A1195 " --> pdb=" O LYS A1191 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1191 through 1196' Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 4.078A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1239 through 1249 Processing helix chain 'A' and resid 1264 through 1273 Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 removed outlier: 3.674A pdb=" N ILE A1355 " --> pdb=" O TRP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 3.558A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.711A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1450 removed outlier: 3.778A pdb=" N THR A1437 " --> pdb=" O THR A1433 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 3.580A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1507 removed outlier: 3.502A pdb=" N PHE A1493 " --> pdb=" O LYS A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1520 removed outlier: 3.693A pdb=" N LEU A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 removed outlier: 3.521A pdb=" N LEU A1527 " --> pdb=" O GLY A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 3.510A pdb=" N LEU A1545 " --> pdb=" O VAL A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.579A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1626 removed outlier: 3.668A pdb=" N GLY A1626 " --> pdb=" O CYS A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1646 Processing helix chain 'A' and resid 1664 through 1669 removed outlier: 3.766A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.718A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1699 removed outlier: 3.681A pdb=" N SER A1699 " --> pdb=" O TRP A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1744 removed outlier: 4.006A pdb=" N GLN A1738 " --> pdb=" O ASN A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1750 removed outlier: 3.718A pdb=" N GLU A1750 " --> pdb=" O VAL A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 4.393A pdb=" N SER A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1783 Processing helix chain 'A' and resid 1787 through 1793 Processing helix chain 'A' and resid 1805 through 1810 removed outlier: 4.132A pdb=" N LEU A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.901A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 6.208A pdb=" N LEU A 559 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU A 567 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1129 through 1134 removed outlier: 6.771A pdb=" N PHE A1117 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1183 through 1188 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AA9, first strand: chain 'A' and resid 1716 through 1719 590 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4073 1.34 - 1.46: 2279 1.46 - 1.58: 6518 1.58 - 1.70: 13 1.70 - 1.82: 120 Bond restraints: 13003 Sorted by residual: bond pdb=" CA LEU A1545 " pdb=" C LEU A1545 " ideal model delta sigma weight residual 1.522 1.503 0.019 1.72e-02 3.38e+03 1.18e+00 bond pdb=" CG LEU A 52 " pdb=" CD1 LEU A 52 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB LYS A 336 " pdb=" CG LYS A 336 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CA ARG A1521 " pdb=" C ARG A1521 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.32e-02 5.74e+03 1.03e+00 bond pdb=" CB GLU A 797 " pdb=" CG GLU A 797 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.74e-01 ... (remaining 12998 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.32: 291 106.32 - 113.24: 7159 113.24 - 120.15: 4613 120.15 - 127.07: 5393 127.07 - 133.99: 116 Bond angle restraints: 17572 Sorted by residual: angle pdb=" N GLY A1523 " pdb=" CA GLY A1523 " pdb=" C GLY A1523 " ideal model delta sigma weight residual 113.18 123.84 -10.66 2.37e+00 1.78e-01 2.02e+01 angle pdb=" N VAL A 156 " pdb=" CA VAL A 156 " pdb=" C VAL A 156 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" N ILE A1777 " pdb=" CA ILE A1777 " pdb=" C ILE A1777 " ideal model delta sigma weight residual 112.96 109.26 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" N GLU A 268 " pdb=" CA GLU A 268 " pdb=" CB GLU A 268 " ideal model delta sigma weight residual 110.12 115.25 -5.13 1.47e+00 4.63e-01 1.22e+01 angle pdb=" N ILE A1640 " pdb=" CA ILE A1640 " pdb=" C ILE A1640 " ideal model delta sigma weight residual 112.96 109.61 3.35 1.00e+00 1.00e+00 1.13e+01 ... (remaining 17567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7158 17.72 - 35.45: 627 35.45 - 53.17: 98 53.17 - 70.89: 29 70.89 - 88.62: 13 Dihedral angle restraints: 7925 sinusoidal: 3270 harmonic: 4655 Sorted by residual: dihedral pdb=" CB CYS A1691 " pdb=" SG CYS A1691 " pdb=" SG CYS A1776 " pdb=" CB CYS A1776 " ideal model delta sinusoidal sigma weight residual -86.00 -142.94 56.94 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA GLU A 21 " pdb=" C GLU A 21 " pdb=" N PHE A 22 " pdb=" CA PHE A 22 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PHE A 300 " pdb=" C PHE A 300 " pdb=" N SER A 301 " pdb=" CA SER A 301 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 7922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1437 0.041 - 0.082: 445 0.082 - 0.122: 125 0.122 - 0.163: 17 0.163 - 0.204: 7 Chirality restraints: 2031 Sorted by residual: chirality pdb=" CA GLU A 21 " pdb=" N GLU A 21 " pdb=" C GLU A 21 " pdb=" CB GLU A 21 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE A1375 " pdb=" CA ILE A1375 " pdb=" CG1 ILE A1375 " pdb=" CG2 ILE A1375 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA THR A1753 " pdb=" N THR A1753 " pdb=" C THR A1753 " pdb=" CB THR A1753 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 2028 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 22 " -0.029 2.00e-02 2.50e+03 2.58e-02 1.16e+01 pdb=" CG PHE A 22 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 22 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 22 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 22 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 22 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 22 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1680 " -0.016 2.00e-02 2.50e+03 1.46e-02 5.35e+00 pdb=" CG TRP A1680 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A1680 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A1680 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1680 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A1680 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A1680 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1680 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1680 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1680 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1528 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C THR A1528 " -0.038 2.00e-02 2.50e+03 pdb=" O THR A1528 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY A1529 " 0.013 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1141 2.74 - 3.28: 14097 3.28 - 3.82: 21012 3.82 - 4.36: 24108 4.36 - 4.90: 39520 Nonbonded interactions: 99878 Sorted by model distance: nonbonded pdb=" OE1 GLU A1150 " pdb=" ND2 ASN A1297 " model vdw 2.199 2.520 nonbonded pdb=" O GLU A1525 " pdb=" OG1 THR A1528 " model vdw 2.208 2.440 nonbonded pdb=" O ILE A1447 " pdb=" OG SER A1450 " model vdw 2.216 2.440 nonbonded pdb=" O ALA A 619 " pdb=" OG SER A 623 " model vdw 2.233 2.440 nonbonded pdb=" OG SER A1537 " pdb=" OE1 GLU A1540 " model vdw 2.238 2.440 ... (remaining 99873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 2.470 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 39.350 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.003 0.035 13003 Z= 0.170 Angle : 0.657 10.660 17572 Z= 0.340 Chirality : 0.043 0.204 2031 Planarity : 0.004 0.041 2196 Dihedral : 14.122 88.617 4885 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1558 helix: 0.73 (0.19), residues: 780 sheet: -0.09 (0.53), residues: 84 loop : -2.27 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1680 HIS 0.008 0.001 HIS A 472 PHE 0.058 0.001 PHE A 22 TYR 0.018 0.001 TYR A 296 ARG 0.007 0.001 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9421 (m-80) cc_final: 0.8962 (m-80) REVERT: A 51 GLU cc_start: 0.7855 (pp20) cc_final: 0.7312 (tm-30) REVERT: A 120 MET cc_start: 0.5225 (ptp) cc_final: 0.4961 (ptp) REVERT: A 635 LEU cc_start: 0.9399 (mm) cc_final: 0.9101 (mm) REVERT: A 702 LEU cc_start: 0.9510 (mt) cc_final: 0.9173 (mt) REVERT: A 919 MET cc_start: 0.9237 (ppp) cc_final: 0.9017 (ppp) REVERT: A 1136 LEU cc_start: 0.9278 (mt) cc_final: 0.8826 (tp) REVERT: A 1141 MET cc_start: 0.8710 (mtm) cc_final: 0.8389 (mtt) REVERT: A 1147 ASP cc_start: 0.8941 (m-30) cc_final: 0.8723 (m-30) REVERT: A 1187 TYR cc_start: 0.8240 (m-10) cc_final: 0.7363 (m-10) REVERT: A 1678 ILE cc_start: 0.8815 (tp) cc_final: 0.8385 (tp) REVERT: A 1680 TRP cc_start: 0.7920 (t-100) cc_final: 0.7657 (t-100) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2271 time to fit residues: 66.9607 Evaluate side-chains 152 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS A1405 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13003 Z= 0.161 Angle : 0.569 8.075 17572 Z= 0.290 Chirality : 0.041 0.187 2031 Planarity : 0.003 0.042 2196 Dihedral : 7.989 87.152 1806 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.21 % Allowed : 8.09 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1558 helix: 0.87 (0.19), residues: 798 sheet: 0.24 (0.53), residues: 80 loop : -2.29 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 116 HIS 0.007 0.001 HIS A 472 PHE 0.041 0.001 PHE A 22 TYR 0.016 0.001 TYR A 296 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9569 (mm) cc_final: 0.9346 (mm) REVERT: A 43 PHE cc_start: 0.9416 (m-80) cc_final: 0.8977 (m-80) REVERT: A 51 GLU cc_start: 0.7805 (pp20) cc_final: 0.7280 (tm-30) REVERT: A 387 MET cc_start: 0.8636 (pmm) cc_final: 0.8356 (pmm) REVERT: A 606 MET cc_start: 0.8904 (mpp) cc_final: 0.8472 (pmm) REVERT: A 702 LEU cc_start: 0.9525 (mt) cc_final: 0.9144 (mt) REVERT: A 708 LYS cc_start: 0.8992 (pttp) cc_final: 0.8296 (ptmm) REVERT: A 836 ASP cc_start: 0.8266 (t0) cc_final: 0.7993 (t0) REVERT: A 851 ARG cc_start: 0.8957 (ptt180) cc_final: 0.8678 (ptt180) REVERT: A 916 LEU cc_start: 0.9545 (mm) cc_final: 0.9314 (mt) REVERT: A 1027 CYS cc_start: 0.8107 (t) cc_final: 0.7800 (t) REVERT: A 1136 LEU cc_start: 0.9274 (mt) cc_final: 0.8842 (tp) REVERT: A 1141 MET cc_start: 0.8693 (mtm) cc_final: 0.8414 (mtt) REVERT: A 1147 ASP cc_start: 0.8934 (m-30) cc_final: 0.8699 (m-30) REVERT: A 1678 ILE cc_start: 0.8850 (tp) cc_final: 0.8498 (tp) REVERT: A 1773 LEU cc_start: 0.8700 (tt) cc_final: 0.8425 (tt) outliers start: 3 outliers final: 1 residues processed: 194 average time/residue: 0.2383 time to fit residues: 67.9987 Evaluate side-chains 144 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 0.0570 chunk 98 optimal weight: 0.0010 chunk 39 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A1231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13003 Z= 0.146 Angle : 0.573 8.845 17572 Z= 0.286 Chirality : 0.041 0.191 2031 Planarity : 0.003 0.040 2196 Dihedral : 7.897 86.461 1806 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1558 helix: 0.95 (0.19), residues: 791 sheet: 0.34 (0.53), residues: 80 loop : -2.21 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 116 HIS 0.006 0.001 HIS A 472 PHE 0.026 0.001 PHE A 22 TYR 0.014 0.001 TYR A 296 ARG 0.006 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9522 (mm) cc_final: 0.9276 (mm) REVERT: A 43 PHE cc_start: 0.9407 (m-80) cc_final: 0.9007 (m-80) REVERT: A 387 MET cc_start: 0.8642 (pmm) cc_final: 0.8352 (pmm) REVERT: A 606 MET cc_start: 0.8898 (mpp) cc_final: 0.8487 (pmm) REVERT: A 629 GLN cc_start: 0.9104 (pt0) cc_final: 0.8731 (pt0) REVERT: A 702 LEU cc_start: 0.9513 (mt) cc_final: 0.9130 (mt) REVERT: A 708 LYS cc_start: 0.8981 (pttp) cc_final: 0.8647 (ptmm) REVERT: A 836 ASP cc_start: 0.8292 (t0) cc_final: 0.8092 (t0) REVERT: A 837 LYS cc_start: 0.8985 (ttpp) cc_final: 0.8712 (ttpp) REVERT: A 851 ARG cc_start: 0.9115 (ptt180) cc_final: 0.8611 (ptt180) REVERT: A 916 LEU cc_start: 0.9597 (mm) cc_final: 0.9366 (mt) REVERT: A 1027 CYS cc_start: 0.8106 (t) cc_final: 0.7779 (t) REVERT: A 1136 LEU cc_start: 0.9250 (mt) cc_final: 0.8840 (tp) REVERT: A 1141 MET cc_start: 0.8717 (mtm) cc_final: 0.8461 (mtt) REVERT: A 1678 ILE cc_start: 0.8842 (tp) cc_final: 0.8502 (tp) REVERT: A 1733 MET cc_start: 0.3107 (tpt) cc_final: 0.2609 (tpt) REVERT: A 1773 LEU cc_start: 0.8678 (tt) cc_final: 0.8358 (tt) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2273 time to fit residues: 65.6491 Evaluate side-chains 147 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 153 optimal weight: 0.0980 chunk 137 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN A1231 HIS A1405 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13003 Z= 0.166 Angle : 0.569 8.221 17572 Z= 0.287 Chirality : 0.041 0.175 2031 Planarity : 0.003 0.041 2196 Dihedral : 7.842 86.267 1806 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1558 helix: 0.96 (0.19), residues: 797 sheet: 0.54 (0.55), residues: 76 loop : -2.21 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 116 HIS 0.005 0.001 HIS A 472 PHE 0.021 0.001 PHE A 22 TYR 0.014 0.001 TYR A 296 ARG 0.012 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9538 (mm) cc_final: 0.9292 (mm) REVERT: A 43 PHE cc_start: 0.9427 (m-80) cc_final: 0.9025 (m-80) REVERT: A 387 MET cc_start: 0.8673 (pmm) cc_final: 0.8393 (pmm) REVERT: A 599 LEU cc_start: 0.9310 (mp) cc_final: 0.8721 (mp) REVERT: A 606 MET cc_start: 0.8900 (mpp) cc_final: 0.8504 (pmm) REVERT: A 702 LEU cc_start: 0.9531 (mt) cc_final: 0.9132 (mt) REVERT: A 708 LYS cc_start: 0.8961 (pttp) cc_final: 0.8721 (ptmm) REVERT: A 851 ARG cc_start: 0.8967 (ptt180) cc_final: 0.8600 (ptt180) REVERT: A 916 LEU cc_start: 0.9603 (mm) cc_final: 0.9362 (mt) REVERT: A 1027 CYS cc_start: 0.8126 (t) cc_final: 0.7815 (t) REVERT: A 1116 LYS cc_start: 0.7969 (tppt) cc_final: 0.7581 (tptt) REVERT: A 1136 LEU cc_start: 0.9308 (mt) cc_final: 0.8825 (tp) REVERT: A 1141 MET cc_start: 0.8717 (mtm) cc_final: 0.8507 (mtt) REVERT: A 1147 ASP cc_start: 0.8848 (m-30) cc_final: 0.8625 (m-30) REVERT: A 1487 ASP cc_start: 0.7112 (t0) cc_final: 0.6818 (t0) REVERT: A 1678 ILE cc_start: 0.9031 (tp) cc_final: 0.8768 (tp) REVERT: A 1773 LEU cc_start: 0.8627 (tt) cc_final: 0.8253 (tt) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2396 time to fit residues: 66.0200 Evaluate side-chains 136 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 114 optimal weight: 0.0970 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN A1179 ASN A1231 HIS A1358 HIS ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13003 Z= 0.216 Angle : 0.598 8.398 17572 Z= 0.303 Chirality : 0.041 0.178 2031 Planarity : 0.003 0.043 2196 Dihedral : 7.903 86.293 1806 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1558 helix: 0.92 (0.19), residues: 800 sheet: 0.36 (0.56), residues: 74 loop : -2.25 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1680 HIS 0.007 0.001 HIS A1358 PHE 0.042 0.001 PHE A 22 TYR 0.015 0.001 TYR A 296 ARG 0.009 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9551 (mm) cc_final: 0.9282 (mm) REVERT: A 43 PHE cc_start: 0.9411 (m-80) cc_final: 0.9007 (m-80) REVERT: A 387 MET cc_start: 0.8655 (pmm) cc_final: 0.8296 (pmm) REVERT: A 565 MET cc_start: 0.8155 (tpt) cc_final: 0.7835 (tpp) REVERT: A 599 LEU cc_start: 0.9340 (mp) cc_final: 0.8959 (mm) REVERT: A 695 TYR cc_start: 0.8966 (t80) cc_final: 0.8714 (t80) REVERT: A 702 LEU cc_start: 0.9490 (mt) cc_final: 0.9124 (mt) REVERT: A 708 LYS cc_start: 0.9110 (pttp) cc_final: 0.8798 (ptmm) REVERT: A 851 ARG cc_start: 0.9065 (ptt180) cc_final: 0.8725 (ptt180) REVERT: A 916 LEU cc_start: 0.9603 (mm) cc_final: 0.9383 (mt) REVERT: A 1027 CYS cc_start: 0.8080 (t) cc_final: 0.7760 (t) REVERT: A 1147 ASP cc_start: 0.8877 (m-30) cc_final: 0.8674 (m-30) REVERT: A 1375 ILE cc_start: 0.8616 (mm) cc_final: 0.8377 (mm) REVERT: A 1773 LEU cc_start: 0.8579 (tt) cc_final: 0.8312 (tt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2424 time to fit residues: 64.6467 Evaluate side-chains 136 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 153 optimal weight: 0.0670 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A1231 HIS A1405 HIS A1689 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13003 Z= 0.150 Angle : 0.591 9.740 17572 Z= 0.292 Chirality : 0.041 0.186 2031 Planarity : 0.003 0.036 2196 Dihedral : 7.809 85.051 1806 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1558 helix: 0.93 (0.19), residues: 805 sheet: 0.28 (0.57), residues: 76 loop : -2.28 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 116 HIS 0.005 0.001 HIS A1405 PHE 0.029 0.001 PHE A 22 TYR 0.014 0.001 TYR A 296 ARG 0.006 0.000 ARG A1499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9549 (mm) cc_final: 0.9297 (mm) REVERT: A 43 PHE cc_start: 0.9413 (m-80) cc_final: 0.9010 (m-80) REVERT: A 51 GLU cc_start: 0.7763 (pp20) cc_final: 0.7176 (tm-30) REVERT: A 387 MET cc_start: 0.8381 (pmm) cc_final: 0.8130 (pmm) REVERT: A 478 MET cc_start: 0.7452 (mtt) cc_final: 0.7135 (mtt) REVERT: A 557 VAL cc_start: 0.9198 (t) cc_final: 0.8935 (p) REVERT: A 565 MET cc_start: 0.8150 (tpt) cc_final: 0.7910 (tpp) REVERT: A 599 LEU cc_start: 0.9325 (mp) cc_final: 0.9010 (mm) REVERT: A 695 TYR cc_start: 0.8913 (t80) cc_final: 0.8610 (t80) REVERT: A 702 LEU cc_start: 0.9465 (mt) cc_final: 0.9075 (mt) REVERT: A 708 LYS cc_start: 0.9069 (pttp) cc_final: 0.8398 (ptmm) REVERT: A 722 GLU cc_start: 0.8863 (pt0) cc_final: 0.8040 (pt0) REVERT: A 837 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8713 (ttpp) REVERT: A 850 GLU cc_start: 0.9400 (tp30) cc_final: 0.8865 (pt0) REVERT: A 851 ARG cc_start: 0.8984 (ptt180) cc_final: 0.8527 (ptt180) REVERT: A 916 LEU cc_start: 0.9597 (mm) cc_final: 0.9370 (mt) REVERT: A 1027 CYS cc_start: 0.8041 (t) cc_final: 0.7725 (t) REVERT: A 1116 LYS cc_start: 0.8050 (tptt) cc_final: 0.7611 (tptt) REVERT: A 1136 LEU cc_start: 0.9258 (mt) cc_final: 0.8844 (tp) REVERT: A 1147 ASP cc_start: 0.8896 (m-30) cc_final: 0.8695 (m-30) REVERT: A 1773 LEU cc_start: 0.8619 (tt) cc_final: 0.8342 (tt) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.2492 time to fit residues: 69.9003 Evaluate side-chains 146 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 85 optimal weight: 0.0870 chunk 153 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS A1689 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13003 Z= 0.149 Angle : 0.604 10.274 17572 Z= 0.299 Chirality : 0.041 0.196 2031 Planarity : 0.003 0.036 2196 Dihedral : 7.792 84.394 1806 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1558 helix: 0.84 (0.19), residues: 809 sheet: 0.27 (0.58), residues: 76 loop : -2.25 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A1680 HIS 0.004 0.001 HIS A 472 PHE 0.026 0.001 PHE A 22 TYR 0.014 0.001 TYR A 296 ARG 0.011 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9581 (mm) cc_final: 0.9309 (mm) REVERT: A 43 PHE cc_start: 0.9384 (m-80) cc_final: 0.8985 (m-80) REVERT: A 51 GLU cc_start: 0.7720 (pp20) cc_final: 0.7171 (tm-30) REVERT: A 120 MET cc_start: 0.5211 (ptp) cc_final: 0.4894 (ptp) REVERT: A 352 PHE cc_start: 0.8914 (t80) cc_final: 0.8558 (t80) REVERT: A 387 MET cc_start: 0.8336 (pmm) cc_final: 0.8105 (pmm) REVERT: A 478 MET cc_start: 0.7473 (mtt) cc_final: 0.7075 (mtt) REVERT: A 557 VAL cc_start: 0.9192 (t) cc_final: 0.8946 (p) REVERT: A 565 MET cc_start: 0.8016 (tpt) cc_final: 0.7791 (tpp) REVERT: A 635 LEU cc_start: 0.9358 (mm) cc_final: 0.9137 (mm) REVERT: A 702 LEU cc_start: 0.9461 (mt) cc_final: 0.9113 (mt) REVERT: A 708 LYS cc_start: 0.9040 (pttp) cc_final: 0.8492 (ptmm) REVERT: A 722 GLU cc_start: 0.8839 (pt0) cc_final: 0.7989 (pt0) REVERT: A 850 GLU cc_start: 0.9423 (tp30) cc_final: 0.8903 (pt0) REVERT: A 851 ARG cc_start: 0.9021 (ptt180) cc_final: 0.8605 (ptt180) REVERT: A 916 LEU cc_start: 0.9575 (mm) cc_final: 0.9201 (mt) REVERT: A 1027 CYS cc_start: 0.8016 (t) cc_final: 0.7704 (t) REVERT: A 1116 LYS cc_start: 0.8200 (tptt) cc_final: 0.7884 (tptt) REVERT: A 1119 LEU cc_start: 0.8899 (tp) cc_final: 0.8696 (tp) REVERT: A 1136 LEU cc_start: 0.9298 (mt) cc_final: 0.8888 (tp) REVERT: A 1141 MET cc_start: 0.8739 (mtm) cc_final: 0.8493 (mtt) REVERT: A 1147 ASP cc_start: 0.8907 (m-30) cc_final: 0.8689 (m-30) REVERT: A 1174 MET cc_start: 0.8576 (ptp) cc_final: 0.8371 (ptt) REVERT: A 1274 MET cc_start: 0.8822 (ttt) cc_final: 0.8393 (mtp) REVERT: A 1279 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8767 (tm-30) REVERT: A 1773 LEU cc_start: 0.8599 (tt) cc_final: 0.8363 (tt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2560 time to fit residues: 68.7582 Evaluate side-chains 141 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 120 optimal weight: 0.0370 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A1231 HIS A1405 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13003 Z= 0.143 Angle : 0.615 11.073 17572 Z= 0.303 Chirality : 0.042 0.194 2031 Planarity : 0.003 0.032 2196 Dihedral : 7.750 83.730 1806 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1558 helix: 0.75 (0.19), residues: 809 sheet: 0.18 (0.58), residues: 76 loop : -2.22 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 116 HIS 0.006 0.001 HIS A1405 PHE 0.038 0.001 PHE A 852 TYR 0.014 0.001 TYR A 296 ARG 0.006 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9604 (mm) cc_final: 0.9323 (mm) REVERT: A 43 PHE cc_start: 0.9378 (m-80) cc_final: 0.8993 (m-80) REVERT: A 51 GLU cc_start: 0.7644 (pp20) cc_final: 0.7114 (tm-30) REVERT: A 338 LYS cc_start: 0.9445 (pptt) cc_final: 0.9152 (pptt) REVERT: A 352 PHE cc_start: 0.8883 (t80) cc_final: 0.8549 (t80) REVERT: A 478 MET cc_start: 0.7422 (mtt) cc_final: 0.7073 (mtt) REVERT: A 557 VAL cc_start: 0.9224 (t) cc_final: 0.8995 (p) REVERT: A 565 MET cc_start: 0.7870 (tpt) cc_final: 0.7642 (tpp) REVERT: A 697 LEU cc_start: 0.9456 (tp) cc_final: 0.9242 (tt) REVERT: A 702 LEU cc_start: 0.9454 (mt) cc_final: 0.9089 (mt) REVERT: A 708 LYS cc_start: 0.9004 (pttp) cc_final: 0.8282 (ptmm) REVERT: A 722 GLU cc_start: 0.8849 (pt0) cc_final: 0.7978 (pt0) REVERT: A 850 GLU cc_start: 0.9306 (tp30) cc_final: 0.8894 (pt0) REVERT: A 851 ARG cc_start: 0.8974 (ptt180) cc_final: 0.8552 (ptt180) REVERT: A 916 LEU cc_start: 0.9517 (mm) cc_final: 0.9210 (mt) REVERT: A 1027 CYS cc_start: 0.7978 (t) cc_final: 0.7669 (t) REVERT: A 1116 LYS cc_start: 0.8259 (tptt) cc_final: 0.7905 (tptt) REVERT: A 1119 LEU cc_start: 0.8879 (tp) cc_final: 0.8664 (tp) REVERT: A 1136 LEU cc_start: 0.9317 (mt) cc_final: 0.8772 (tp) REVERT: A 1141 MET cc_start: 0.8693 (mtm) cc_final: 0.8475 (mtt) REVERT: A 1147 ASP cc_start: 0.8895 (m-30) cc_final: 0.8681 (m-30) REVERT: A 1174 MET cc_start: 0.8591 (ptp) cc_final: 0.8389 (ptt) REVERT: A 1274 MET cc_start: 0.8797 (ttt) cc_final: 0.8336 (tpp) REVERT: A 1279 GLN cc_start: 0.9176 (tp-100) cc_final: 0.8798 (tm-30) REVERT: A 1487 ASP cc_start: 0.7044 (t0) cc_final: 0.6691 (t0) REVERT: A 1773 LEU cc_start: 0.8619 (tt) cc_final: 0.8348 (tt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2487 time to fit residues: 66.2128 Evaluate side-chains 146 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.8980 chunk 142 optimal weight: 0.0050 chunk 146 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 62 optimal weight: 0.0030 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS A1297 ASN A1689 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13003 Z= 0.138 Angle : 0.619 11.325 17572 Z= 0.302 Chirality : 0.042 0.204 2031 Planarity : 0.003 0.059 2196 Dihedral : 7.723 83.280 1806 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1558 helix: 0.81 (0.19), residues: 809 sheet: 0.03 (0.57), residues: 77 loop : -2.17 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 116 HIS 0.003 0.001 HIS A 472 PHE 0.035 0.001 PHE A 852 TYR 0.014 0.001 TYR A 296 ARG 0.005 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9598 (mm) cc_final: 0.9369 (mm) REVERT: A 43 PHE cc_start: 0.9348 (m-80) cc_final: 0.9001 (m-80) REVERT: A 51 GLU cc_start: 0.7647 (pp20) cc_final: 0.7131 (tm-30) REVERT: A 338 LYS cc_start: 0.9457 (pptt) cc_final: 0.9154 (pptt) REVERT: A 478 MET cc_start: 0.7376 (mtt) cc_final: 0.7028 (mtt) REVERT: A 557 VAL cc_start: 0.9217 (t) cc_final: 0.8993 (p) REVERT: A 565 MET cc_start: 0.7815 (tpt) cc_final: 0.7609 (tpp) REVERT: A 635 LEU cc_start: 0.9371 (mm) cc_final: 0.9114 (mm) REVERT: A 702 LEU cc_start: 0.9445 (mt) cc_final: 0.9082 (mt) REVERT: A 708 LYS cc_start: 0.9024 (pttp) cc_final: 0.8264 (ptmm) REVERT: A 722 GLU cc_start: 0.8855 (pt0) cc_final: 0.7981 (pt0) REVERT: A 837 LYS cc_start: 0.8994 (ttpp) cc_final: 0.8769 (ttpp) REVERT: A 850 GLU cc_start: 0.9310 (tp30) cc_final: 0.8876 (pt0) REVERT: A 851 ARG cc_start: 0.8943 (ptt180) cc_final: 0.8462 (ptt180) REVERT: A 916 LEU cc_start: 0.9515 (mm) cc_final: 0.9297 (mt) REVERT: A 1027 CYS cc_start: 0.8037 (t) cc_final: 0.7762 (t) REVERT: A 1116 LYS cc_start: 0.8221 (tptt) cc_final: 0.7921 (tptt) REVERT: A 1119 LEU cc_start: 0.8853 (tp) cc_final: 0.8643 (tp) REVERT: A 1136 LEU cc_start: 0.9276 (mt) cc_final: 0.8676 (tt) REVERT: A 1141 MET cc_start: 0.8662 (mtm) cc_final: 0.8450 (mtt) REVERT: A 1174 MET cc_start: 0.8558 (ptp) cc_final: 0.8350 (ptt) REVERT: A 1274 MET cc_start: 0.8789 (ttt) cc_final: 0.8335 (tpp) REVERT: A 1279 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8939 (tm-30) REVERT: A 1290 MET cc_start: 0.6862 (tmm) cc_final: 0.6092 (tmm) REVERT: A 1375 ILE cc_start: 0.8285 (mm) cc_final: 0.7973 (mm) REVERT: A 1487 ASP cc_start: 0.7141 (t0) cc_final: 0.6783 (t0) REVERT: A 1773 LEU cc_start: 0.8646 (tt) cc_final: 0.8360 (tt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2452 time to fit residues: 65.3850 Evaluate side-chains 143 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN A 607 ASN A1231 HIS A1358 HIS A1405 HIS A1689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13003 Z= 0.171 Angle : 0.639 11.979 17572 Z= 0.314 Chirality : 0.042 0.201 2031 Planarity : 0.004 0.064 2196 Dihedral : 7.757 83.732 1806 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1558 helix: 0.85 (0.19), residues: 807 sheet: 0.22 (0.56), residues: 76 loop : -2.18 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 116 HIS 0.006 0.001 HIS A1405 PHE 0.034 0.001 PHE A 852 TYR 0.016 0.001 TYR A 695 ARG 0.014 0.001 ARG A 614 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9422 (m-80) cc_final: 0.9019 (m-80) REVERT: A 51 GLU cc_start: 0.7636 (pp20) cc_final: 0.7094 (tm-30) REVERT: A 338 LYS cc_start: 0.9497 (pptt) cc_final: 0.9167 (pptt) REVERT: A 478 MET cc_start: 0.7504 (mtt) cc_final: 0.7119 (mtt) REVERT: A 557 VAL cc_start: 0.9237 (t) cc_final: 0.9016 (p) REVERT: A 635 LEU cc_start: 0.9395 (mm) cc_final: 0.9184 (mm) REVERT: A 702 LEU cc_start: 0.9490 (mt) cc_final: 0.9125 (mt) REVERT: A 708 LYS cc_start: 0.9027 (pttp) cc_final: 0.8283 (ptmm) REVERT: A 722 GLU cc_start: 0.8860 (pt0) cc_final: 0.8004 (pt0) REVERT: A 850 GLU cc_start: 0.9317 (tp30) cc_final: 0.8867 (pt0) REVERT: A 851 ARG cc_start: 0.8942 (ptt180) cc_final: 0.8456 (ptt180) REVERT: A 916 LEU cc_start: 0.9456 (mm) cc_final: 0.9208 (mt) REVERT: A 1026 MET cc_start: 0.7706 (mmp) cc_final: 0.6734 (mtm) REVERT: A 1116 LYS cc_start: 0.8274 (tptt) cc_final: 0.7994 (tptt) REVERT: A 1119 LEU cc_start: 0.8917 (tp) cc_final: 0.8701 (tp) REVERT: A 1141 MET cc_start: 0.8696 (mtm) cc_final: 0.8485 (mtt) REVERT: A 1274 MET cc_start: 0.8790 (ttt) cc_final: 0.8365 (tpp) REVERT: A 1290 MET cc_start: 0.6998 (tmm) cc_final: 0.6154 (tmm) REVERT: A 1375 ILE cc_start: 0.8526 (mm) cc_final: 0.8218 (mm) REVERT: A 1773 LEU cc_start: 0.8624 (tt) cc_final: 0.8349 (tt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2331 time to fit residues: 59.3133 Evaluate side-chains 130 residues out of total 1462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.0030 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1689 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.087930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064691 restraints weight = 60319.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066459 restraints weight = 42271.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067643 restraints weight = 32424.901| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13003 Z= 0.207 Angle : 0.657 11.946 17572 Z= 0.327 Chirality : 0.043 0.215 2031 Planarity : 0.004 0.054 2196 Dihedral : 7.874 84.430 1806 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1558 helix: 0.81 (0.19), residues: 805 sheet: 0.34 (0.56), residues: 74 loop : -2.20 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A1680 HIS 0.004 0.001 HIS A 472 PHE 0.034 0.001 PHE A 852 TYR 0.016 0.001 TYR A 296 ARG 0.009 0.001 ARG A 614 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2440.56 seconds wall clock time: 45 minutes 26.82 seconds (2726.82 seconds total)