Starting phenix.real_space_refine on Wed Mar 4 11:13:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kle_0709/03_2026/6kle_0709.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kle_0709/03_2026/6kle_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kle_0709/03_2026/6kle_0709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kle_0709/03_2026/6kle_0709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kle_0709/03_2026/6kle_0709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kle_0709/03_2026/6kle_0709.map" } resolution = 4.5 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 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ARG:plan': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'HIS:plan': 2, 'PHE:plan': 3} 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: 2.86, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 1.08 Conformation dependent library (CDL) restraints added in 462.3 milliseconds 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: 0.49 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: 2.07 Time building geometry restraints manager: 1.39 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: 0.00 - 2.13: 17247 2.13 - 4.26: 279 4.26 - 6.40: 39 6.40 - 8.53: 5 8.53 - 10.66: 2 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 3.120 nonbonded pdb=" O GLU A1525 " pdb=" OG1 THR A1528 " model vdw 2.208 3.040 nonbonded pdb=" O ILE A1447 " pdb=" OG SER A1450 " model vdw 2.216 3.040 nonbonded pdb=" O ALA A 619 " pdb=" OG SER A 623 " model vdw 2.233 3.040 nonbonded pdb=" OG SER A1537 " pdb=" OE1 GLU A1540 " model vdw 2.238 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.530 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- 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 0.083 13009 Z= 0.137 Angle : 0.662 10.660 17579 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG A 614 TYR 0.018 0.001 TYR A 296 PHE 0.058 0.001 PHE A 22 TRP 0.040 0.002 TRP A1680 HIS 0.008 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00268 (13003) covalent geometry : angle 0.65744 (17572) SS BOND : bond 0.00218 ( 2) SS BOND : angle 1.08416 ( 4) hydrogen bonds : bond 0.12647 ( 590) hydrogen bonds : angle 5.38216 ( 1704) metal coordination : bond 0.06855 ( 4) metal coordination : angle 5.95700 ( 3) *********************** 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 to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.481 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: 0.7311 (tm-30) REVERT: A 120 MET cc_start: 0.5225 (ptp) cc_final: 0.4956 (ptp) REVERT: A 635 LEU cc_start: 0.9399 (mm) cc_final: 0.9102 (mm) REVERT: A 702 LEU cc_start: 0.9510 (mt) cc_final: 0.9169 (mt) REVERT: A 1136 LEU cc_start: 0.9278 (mt) cc_final: 0.8825 (tp) REVERT: A 1141 MET cc_start: 0.8710 (mtm) cc_final: 0.8384 (mtt) REVERT: A 1147 ASP cc_start: 0.8941 (m-30) cc_final: 0.8620 (m-30) REVERT: A 1187 TYR cc_start: 0.8240 (m-10) cc_final: 0.7364 (m-10) REVERT: A 1678 ILE cc_start: 0.8815 (tp) cc_final: 0.8386 (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: 0.0994 time to fit residues: 29.8201 Evaluate side-chains 151 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 800 ASN A1231 HIS A1405 HIS A1406 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.088093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065042 restraints weight = 58156.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066654 restraints weight = 42319.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.067730 restraints weight = 33207.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068592 restraints weight = 27863.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.069223 restraints weight = 24269.627| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13009 Z= 0.185 Angle : 0.640 8.086 17579 Z= 0.330 Chirality : 0.043 0.162 2031 Planarity : 0.004 0.053 2196 Dihedral : 8.181 87.378 1806 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.14 % Allowed : 8.79 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1558 helix: 0.75 (0.19), residues: 793 sheet: 0.17 (0.55), residues: 74 loop : -2.27 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 851 TYR 0.017 0.002 TYR A 296 PHE 0.037 0.002 PHE A 22 TRP 0.025 0.002 TRP A1680 HIS 0.008 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00389 (13003) covalent geometry : angle 0.63756 (17572) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.27158 ( 4) hydrogen bonds : bond 0.03717 ( 590) hydrogen bonds : angle 4.35414 ( 1704) metal coordination : bond 0.01090 ( 4) metal coordination : angle 4.17664 ( 3) *********************** 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 185 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.526 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 43 PHE cc_start: 0.9513 (m-80) cc_final: 0.9136 (m-80) REVERT: A 51 GLU cc_start: 0.7935 (pp20) cc_final: 0.7332 (tm-30) REVERT: A 387 MET cc_start: 0.8646 (pmm) cc_final: 0.8377 (pmm) REVERT: A 595 MET cc_start: 0.8818 (tpt) cc_final: 0.8593 (mmm) REVERT: A 695 TYR cc_start: 0.9468 (t80) cc_final: 0.8948 (t80) REVERT: A 702 LEU cc_start: 0.9383 (mt) cc_final: 0.8989 (mt) REVERT: A 708 LYS cc_start: 0.8976 (pttp) cc_final: 0.8353 (ptmm) REVERT: A 836 ASP cc_start: 0.8285 (t0) cc_final: 0.8008 (t0) REVERT: A 848 MET cc_start: 0.8582 (mmp) cc_final: 0.8336 (mmp) REVERT: A 851 ARG cc_start: 0.8850 (ptt180) cc_final: 0.8562 (ptt180) REVERT: A 1027 CYS cc_start: 0.7944 (t) cc_final: 0.7671 (t) REVERT: A 1141 MET cc_start: 0.9091 (mtm) cc_final: 0.8785 (mtt) REVERT: A 1147 ASP cc_start: 0.9218 (m-30) cc_final: 0.8994 (m-30) REVERT: A 1210 LEU cc_start: 0.8457 (mm) cc_final: 0.8246 (mm) REVERT: A 1274 MET cc_start: 0.9001 (ttm) cc_final: 0.8691 (ttt) REVERT: A 1375 ILE cc_start: 0.9012 (mm) cc_final: 0.8741 (mm) REVERT: A 1530 PHE cc_start: 0.8323 (m-10) cc_final: 0.8064 (m-10) REVERT: A 1678 ILE cc_start: 0.8979 (tp) cc_final: 0.8614 (tp) REVERT: A 1733 MET cc_start: 0.3649 (tpt) cc_final: 0.3038 (tpt) REVERT: A 1773 LEU cc_start: 0.8893 (tt) cc_final: 0.8596 (tt) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.1066 time to fit residues: 29.0503 Evaluate side-chains 137 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 120 optimal weight: 0.0980 chunk 5 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 476 GLN A1231 HIS A1665 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.089821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065835 restraints weight = 59552.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067717 restraints weight = 41257.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069044 restraints weight = 31287.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069900 restraints weight = 25629.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070592 restraints weight = 22225.711| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13009 Z= 0.117 Angle : 0.610 8.868 17579 Z= 0.306 Chirality : 0.042 0.179 2031 Planarity : 0.003 0.042 2196 Dihedral : 8.083 86.240 1806 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1558 helix: 0.80 (0.19), residues: 791 sheet: 0.43 (0.56), residues: 74 loop : -2.28 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 614 TYR 0.014 0.001 TYR A 296 PHE 0.026 0.001 PHE A 22 TRP 0.018 0.001 TRP A 116 HIS 0.009 0.001 HIS A 648 Details of bonding type rmsd covalent geometry : bond 0.00250 (13003) covalent geometry : angle 0.60814 (17572) SS BOND : bond 0.00400 ( 2) SS BOND : angle 0.85815 ( 4) hydrogen bonds : bond 0.03373 ( 590) hydrogen bonds : angle 4.11143 ( 1704) metal coordination : bond 0.01262 ( 4) metal coordination : angle 3.81637 ( 3) *********************** 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 186 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.387 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 43 PHE cc_start: 0.9486 (m-80) cc_final: 0.9132 (m-80) REVERT: A 51 GLU cc_start: 0.7805 (pp20) cc_final: 0.7204 (tm-30) REVERT: A 394 LEU cc_start: 0.8964 (tp) cc_final: 0.8713 (tt) REVERT: A 695 TYR cc_start: 0.9257 (t80) cc_final: 0.8859 (t80) REVERT: A 702 LEU cc_start: 0.9500 (mt) cc_final: 0.9095 (mt) REVERT: A 708 LYS cc_start: 0.8995 (pttp) cc_final: 0.8418 (ptmm) REVERT: A 1027 CYS cc_start: 0.7884 (t) cc_final: 0.7606 (t) REVERT: A 1097 TYR cc_start: 0.7756 (t80) cc_final: 0.7498 (t80) REVERT: A 1136 LEU cc_start: 0.9408 (mt) cc_final: 0.8962 (tp) REVERT: A 1141 MET cc_start: 0.8990 (mtm) cc_final: 0.8692 (mtt) REVERT: A 1147 ASP cc_start: 0.9143 (m-30) cc_final: 0.8902 (m-30) REVERT: A 1210 LEU cc_start: 0.8280 (mm) cc_final: 0.8060 (mm) REVERT: A 1274 MET cc_start: 0.8951 (ttm) cc_final: 0.8633 (ttt) REVERT: A 1678 ILE cc_start: 0.9035 (tp) cc_final: 0.8652 (tp) REVERT: A 1681 ASP cc_start: 0.9145 (m-30) cc_final: 0.8941 (m-30) REVERT: A 1773 LEU cc_start: 0.8752 (tt) cc_final: 0.8397 (tt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0908 time to fit residues: 25.5068 Evaluate side-chains 146 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 122 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.090031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066070 restraints weight = 59945.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067805 restraints weight = 41405.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069177 restraints weight = 31967.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.069894 restraints weight = 26013.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070821 restraints weight = 22698.334| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13009 Z= 0.116 Angle : 0.595 9.041 17579 Z= 0.300 Chirality : 0.042 0.171 2031 Planarity : 0.003 0.041 2196 Dihedral : 8.013 85.823 1806 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.21), residues: 1558 helix: 0.80 (0.19), residues: 791 sheet: 0.45 (0.56), residues: 76 loop : -2.26 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 614 TYR 0.014 0.001 TYR A 296 PHE 0.032 0.001 PHE A1683 TRP 0.016 0.001 TRP A 116 HIS 0.007 0.001 HIS A 648 Details of bonding type rmsd covalent geometry : bond 0.00249 (13003) covalent geometry : angle 0.59341 (17572) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.97653 ( 4) hydrogen bonds : bond 0.03166 ( 590) hydrogen bonds : angle 4.05964 ( 1704) metal coordination : bond 0.01169 ( 4) metal coordination : angle 3.73349 ( 3) *********************** 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 186 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.501 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 43 PHE cc_start: 0.9513 (m-80) cc_final: 0.9146 (m-80) REVERT: A 695 TYR cc_start: 0.9257 (t80) cc_final: 0.8964 (t80) REVERT: A 702 LEU cc_start: 0.9463 (mt) cc_final: 0.9050 (mt) REVERT: A 708 LYS cc_start: 0.8945 (pttp) cc_final: 0.8390 (ptmm) REVERT: A 848 MET cc_start: 0.8518 (mmp) cc_final: 0.8225 (mmm) REVERT: A 851 ARG cc_start: 0.8964 (ptt180) cc_final: 0.8700 (ptt180) REVERT: A 1027 CYS cc_start: 0.7908 (t) cc_final: 0.7659 (t) REVERT: A 1116 LYS cc_start: 0.8284 (tptt) cc_final: 0.7953 (tptt) REVERT: A 1136 LEU cc_start: 0.9407 (mt) cc_final: 0.8955 (tp) REVERT: A 1141 MET cc_start: 0.9045 (mtm) cc_final: 0.8767 (mtt) REVERT: A 1147 ASP cc_start: 0.9175 (m-30) cc_final: 0.8932 (m-30) REVERT: A 1210 LEU cc_start: 0.8364 (mm) cc_final: 0.8120 (mm) REVERT: A 1375 ILE cc_start: 0.8742 (mm) cc_final: 0.8412 (mm) REVERT: A 1678 ILE cc_start: 0.9198 (tp) cc_final: 0.8885 (tp) REVERT: A 1680 TRP cc_start: 0.8849 (t-100) cc_final: 0.8318 (t-100) REVERT: A 1681 ASP cc_start: 0.9259 (m-30) cc_final: 0.8979 (m-30) REVERT: A 1773 LEU cc_start: 0.8797 (tt) cc_final: 0.8435 (tt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0991 time to fit residues: 27.8010 Evaluate side-chains 140 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.090131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066497 restraints weight = 59670.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068325 restraints weight = 41365.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069623 restraints weight = 31698.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.070506 restraints weight = 25958.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.071236 restraints weight = 22480.607| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13009 Z= 0.112 Angle : 0.607 9.189 17579 Z= 0.303 Chirality : 0.042 0.176 2031 Planarity : 0.003 0.036 2196 Dihedral : 7.963 85.458 1806 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1558 helix: 0.79 (0.18), residues: 797 sheet: 0.44 (0.57), residues: 74 loop : -2.32 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 614 TYR 0.014 0.001 TYR A 296 PHE 0.046 0.001 PHE A 22 TRP 0.016 0.001 TRP A 116 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00242 (13003) covalent geometry : angle 0.60537 (17572) SS BOND : bond 0.00523 ( 2) SS BOND : angle 1.32312 ( 4) hydrogen bonds : bond 0.03069 ( 590) hydrogen bonds : angle 3.99547 ( 1704) metal coordination : bond 0.01454 ( 4) metal coordination : angle 3.67586 ( 3) *********************** 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 184 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9495 (m-80) cc_final: 0.9154 (m-80) REVERT: A 51 GLU cc_start: 0.7788 (pp20) cc_final: 0.7185 (tm-30) REVERT: A 695 TYR cc_start: 0.9289 (t80) cc_final: 0.9047 (t80) REVERT: A 699 VAL cc_start: 0.9447 (t) cc_final: 0.9212 (t) REVERT: A 702 LEU cc_start: 0.9372 (mt) cc_final: 0.8937 (mt) REVERT: A 708 LYS cc_start: 0.8949 (pttp) cc_final: 0.8335 (ptmm) REVERT: A 1027 CYS cc_start: 0.7888 (t) cc_final: 0.7634 (t) REVERT: A 1097 TYR cc_start: 0.7903 (t80) cc_final: 0.7565 (t80) REVERT: A 1116 LYS cc_start: 0.8277 (tptt) cc_final: 0.7924 (tptt) REVERT: A 1136 LEU cc_start: 0.9399 (mt) cc_final: 0.8955 (tp) REVERT: A 1141 MET cc_start: 0.8995 (mtm) cc_final: 0.8743 (mtt) REVERT: A 1147 ASP cc_start: 0.9282 (m-30) cc_final: 0.8876 (m-30) REVERT: A 1174 MET cc_start: 0.8728 (ptp) cc_final: 0.8524 (ptt) REVERT: A 1304 LEU cc_start: 0.9265 (tt) cc_final: 0.8819 (tt) REVERT: A 1487 ASP cc_start: 0.7126 (t0) cc_final: 0.6686 (t0) REVERT: A 1680 TRP cc_start: 0.8844 (t-100) cc_final: 0.8303 (t-100) REVERT: A 1773 LEU cc_start: 0.8720 (tt) cc_final: 0.8444 (tt) REVERT: A 1784 GLU cc_start: 0.8613 (mp0) cc_final: 0.8390 (pm20) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.0989 time to fit residues: 27.3758 Evaluate side-chains 140 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 72 optimal weight: 0.0170 chunk 132 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- 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** A1231 HIS 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 = 0.3708 r_free = 0.3708 target = 0.089709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066655 restraints weight = 57440.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068369 restraints weight = 42203.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069512 restraints weight = 32770.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.070410 restraints weight = 27184.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.071084 restraints weight = 23549.603| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13009 Z= 0.114 Angle : 0.610 9.784 17579 Z= 0.305 Chirality : 0.042 0.188 2031 Planarity : 0.003 0.036 2196 Dihedral : 7.938 85.261 1806 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1558 helix: 0.79 (0.18), residues: 796 sheet: 0.32 (0.58), residues: 74 loop : -2.27 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.014 0.001 TYR A 296 PHE 0.028 0.001 PHE A 22 TRP 0.016 0.001 TRP A 116 HIS 0.005 0.001 HIS A 648 Details of bonding type rmsd covalent geometry : bond 0.00247 (13003) covalent geometry : angle 0.60805 (17572) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.28112 ( 4) hydrogen bonds : bond 0.03035 ( 590) hydrogen bonds : angle 4.03178 ( 1704) metal coordination : bond 0.00898 ( 4) metal coordination : angle 3.30247 ( 3) *********************** 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 185 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.481 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 43 PHE cc_start: 0.9502 (m-80) cc_final: 0.9156 (m-80) REVERT: A 51 GLU cc_start: 0.7819 (pp20) cc_final: 0.7240 (tm-30) REVERT: A 478 MET cc_start: 0.7708 (mtt) cc_final: 0.7332 (mtt) REVERT: A 557 VAL cc_start: 0.9325 (t) cc_final: 0.9054 (p) REVERT: A 565 MET cc_start: 0.8247 (tpt) cc_final: 0.8037 (tpp) REVERT: A 695 TYR cc_start: 0.9351 (t80) cc_final: 0.9096 (t80) REVERT: A 702 LEU cc_start: 0.9330 (mt) cc_final: 0.8925 (mt) REVERT: A 708 LYS cc_start: 0.8893 (pttp) cc_final: 0.7818 (ptmm) REVERT: A 851 ARG cc_start: 0.8996 (ptt180) cc_final: 0.8683 (ptt180) REVERT: A 1027 CYS cc_start: 0.7988 (t) cc_final: 0.7712 (t) REVERT: A 1116 LYS cc_start: 0.8316 (tptt) cc_final: 0.8021 (tptt) REVERT: A 1136 LEU cc_start: 0.9383 (mt) cc_final: 0.8988 (tp) REVERT: A 1141 MET cc_start: 0.9070 (mtm) cc_final: 0.8813 (mtt) REVERT: A 1147 ASP cc_start: 0.9196 (m-30) cc_final: 0.8959 (m-30) REVERT: A 1279 GLN cc_start: 0.9229 (tp-100) cc_final: 0.8618 (pp30) REVERT: A 1375 ILE cc_start: 0.8830 (mm) cc_final: 0.8446 (mm) REVERT: A 1487 ASP cc_start: 0.7269 (t0) cc_final: 0.6813 (t0) REVERT: A 1680 TRP cc_start: 0.9031 (t-100) cc_final: 0.8317 (t-100) REVERT: A 1773 LEU cc_start: 0.8788 (tt) cc_final: 0.8536 (tt) REVERT: A 1782 MET cc_start: 0.8908 (mtp) cc_final: 0.8686 (mtt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1104 time to fit residues: 30.0707 Evaluate side-chains 142 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 131 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** 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 = 0.3661 r_free = 0.3661 target = 0.087197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063955 restraints weight = 59376.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065703 restraints weight = 41793.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066874 restraints weight = 32151.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067792 restraints weight = 26538.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068408 restraints weight = 22979.854| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13009 Z= 0.161 Angle : 0.641 10.281 17579 Z= 0.324 Chirality : 0.042 0.171 2031 Planarity : 0.004 0.052 2196 Dihedral : 8.000 86.511 1806 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.21), residues: 1558 helix: 0.73 (0.18), residues: 799 sheet: 0.25 (0.58), residues: 74 loop : -2.24 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 264 TYR 0.015 0.001 TYR A 296 PHE 0.023 0.001 PHE A 22 TRP 0.022 0.002 TRP A 116 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00344 (13003) covalent geometry : angle 0.63810 (17572) SS BOND : bond 0.00317 ( 2) SS BOND : angle 1.56017 ( 4) hydrogen bonds : bond 0.03248 ( 590) hydrogen bonds : angle 4.15596 ( 1704) metal coordination : bond 0.00907 ( 4) metal coordination : angle 4.81688 ( 3) *********************** 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 175 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.482 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 43 PHE cc_start: 0.9506 (m-80) cc_final: 0.9125 (m-80) REVERT: A 478 MET cc_start: 0.7591 (mtt) cc_final: 0.7229 (mtt) REVERT: A 635 LEU cc_start: 0.9537 (mm) cc_final: 0.9333 (mm) REVERT: A 695 TYR cc_start: 0.9276 (t80) cc_final: 0.8822 (t80) REVERT: A 702 LEU cc_start: 0.9426 (mt) cc_final: 0.9017 (mt) REVERT: A 708 LYS cc_start: 0.8973 (pttp) cc_final: 0.8041 (ptmm) REVERT: A 844 CYS cc_start: 0.8761 (t) cc_final: 0.8559 (p) REVERT: A 851 ARG cc_start: 0.8873 (ptt180) cc_final: 0.8653 (ptt180) REVERT: A 1027 CYS cc_start: 0.8040 (t) cc_final: 0.7708 (t) REVERT: A 1116 LYS cc_start: 0.8402 (tptt) cc_final: 0.7820 (mmtt) REVERT: A 1136 LEU cc_start: 0.9450 (mt) cc_final: 0.9025 (tp) REVERT: A 1141 MET cc_start: 0.8993 (mtm) cc_final: 0.8774 (mtt) REVERT: A 1147 ASP cc_start: 0.9217 (m-30) cc_final: 0.8977 (m-30) REVERT: A 1210 LEU cc_start: 0.8203 (mm) cc_final: 0.7981 (mm) REVERT: A 1279 GLN cc_start: 0.9224 (tp-100) cc_final: 0.8928 (pp30) REVERT: A 1375 ILE cc_start: 0.8991 (mm) cc_final: 0.8707 (mm) REVERT: A 1680 TRP cc_start: 0.9093 (t-100) cc_final: 0.8429 (t-100) REVERT: A 1773 LEU cc_start: 0.8839 (tt) cc_final: 0.8595 (tt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1052 time to fit residues: 27.6424 Evaluate side-chains 141 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 141 optimal weight: 0.0770 chunk 140 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 8 optimal weight: 6.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- 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 910 HIS A1231 HIS ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3708 r_free = 0.3708 target = 0.089681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066710 restraints weight = 57059.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068338 restraints weight = 41315.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069469 restraints weight = 32377.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.070370 restraints weight = 27033.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070991 restraints weight = 23498.168| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13009 Z= 0.111 Angle : 0.639 10.592 17579 Z= 0.312 Chirality : 0.042 0.167 2031 Planarity : 0.003 0.046 2196 Dihedral : 7.891 86.313 1806 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.07 % Allowed : 1.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1558 helix: 0.72 (0.18), residues: 795 sheet: 0.49 (0.57), residues: 74 loop : -2.17 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 614 TYR 0.014 0.001 TYR A 296 PHE 0.024 0.001 PHE A 22 TRP 0.016 0.001 TRP A 116 HIS 0.006 0.001 HIS A1231 Details of bonding type rmsd covalent geometry : bond 0.00232 (13003) covalent geometry : angle 0.63696 (17572) SS BOND : bond 0.00347 ( 2) SS BOND : angle 1.15420 ( 4) hydrogen bonds : bond 0.03035 ( 590) hydrogen bonds : angle 4.03447 ( 1704) metal coordination : bond 0.01988 ( 4) metal coordination : angle 3.45865 ( 3) *********************** 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 187 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.479 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 43 PHE cc_start: 0.9495 (m-80) cc_final: 0.9143 (m-80) REVERT: A 338 LYS cc_start: 0.9508 (pptt) cc_final: 0.9159 (pptt) REVERT: A 352 PHE cc_start: 0.9322 (t80) cc_final: 0.9031 (t80) REVERT: A 478 MET cc_start: 0.7576 (mtt) cc_final: 0.7227 (mtt) REVERT: A 599 LEU cc_start: 0.9611 (mm) cc_final: 0.9353 (mm) REVERT: A 629 GLN cc_start: 0.8729 (pt0) cc_final: 0.8345 (pt0) REVERT: A 695 TYR cc_start: 0.9309 (t80) cc_final: 0.8960 (t80) REVERT: A 702 LEU cc_start: 0.9299 (mt) cc_final: 0.8841 (mt) REVERT: A 708 LYS cc_start: 0.8816 (pttp) cc_final: 0.7769 (ptmm) REVERT: A 910 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7637 (m170) REVERT: A 1026 MET cc_start: 0.7671 (mmp) cc_final: 0.6923 (mtm) REVERT: A 1097 TYR cc_start: 0.7610 (t80) cc_final: 0.7406 (t80) REVERT: A 1116 LYS cc_start: 0.8341 (tptt) cc_final: 0.7814 (mmtt) REVERT: A 1136 LEU cc_start: 0.9442 (mt) cc_final: 0.8992 (tp) REVERT: A 1141 MET cc_start: 0.9021 (mtm) cc_final: 0.8776 (mtt) REVERT: A 1147 ASP cc_start: 0.9183 (m-30) cc_final: 0.8947 (m-30) REVERT: A 1210 LEU cc_start: 0.8255 (mm) cc_final: 0.8041 (mm) REVERT: A 1279 GLN cc_start: 0.9222 (tp-100) cc_final: 0.8914 (pp30) REVERT: A 1304 LEU cc_start: 0.9322 (tt) cc_final: 0.8919 (tt) REVERT: A 1375 ILE cc_start: 0.8908 (mm) cc_final: 0.8679 (mm) REVERT: A 1487 ASP cc_start: 0.7153 (t0) cc_final: 0.6707 (t0) REVERT: A 1530 PHE cc_start: 0.8333 (m-10) cc_final: 0.8096 (m-10) REVERT: A 1773 LEU cc_start: 0.8818 (tt) cc_final: 0.8543 (tt) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.1055 time to fit residues: 29.3239 Evaluate side-chains 143 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 131 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1231 HIS A1405 HIS A1689 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.086185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063106 restraints weight = 59836.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.064816 restraints weight = 42244.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066011 restraints weight = 32513.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066847 restraints weight = 26790.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067516 restraints weight = 23252.433| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13009 Z= 0.191 Angle : 0.703 11.638 17579 Z= 0.357 Chirality : 0.044 0.179 2031 Planarity : 0.004 0.054 2196 Dihedral : 8.083 88.347 1806 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.14 % Allowed : 1.05 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.21), residues: 1558 helix: 0.61 (0.18), residues: 798 sheet: 0.32 (0.56), residues: 74 loop : -2.19 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 19 TYR 0.017 0.002 TYR A 296 PHE 0.027 0.002 PHE A1357 TRP 0.032 0.002 TRP A 116 HIS 0.011 0.001 HIS A 910 Details of bonding type rmsd covalent geometry : bond 0.00404 (13003) covalent geometry : angle 0.69849 (17572) SS BOND : bond 0.00472 ( 2) SS BOND : angle 2.85018 ( 4) hydrogen bonds : bond 0.03505 ( 590) hydrogen bonds : angle 4.38842 ( 1704) metal coordination : bond 0.00860 ( 4) metal coordination : angle 4.88218 ( 3) *********************** 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 168 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9502 (m-80) cc_final: 0.9139 (m-80) REVERT: A 565 MET cc_start: 0.8558 (tpt) cc_final: 0.8302 (tpp) REVERT: A 595 MET cc_start: 0.8921 (tpt) cc_final: 0.8694 (mmm) REVERT: A 629 GLN cc_start: 0.8714 (pt0) cc_final: 0.8261 (pt0) REVERT: A 695 TYR cc_start: 0.9256 (t80) cc_final: 0.8743 (t80) REVERT: A 702 LEU cc_start: 0.9418 (mt) cc_final: 0.8958 (mt) REVERT: A 708 LYS cc_start: 0.9071 (pttp) cc_final: 0.8331 (ptmm) REVERT: A 850 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8195 (mt-10) REVERT: A 851 ARG cc_start: 0.8738 (ptt180) cc_final: 0.8185 (ptt90) REVERT: A 910 HIS cc_start: 0.8368 (m-70) cc_final: 0.8076 (m170) REVERT: A 1026 MET cc_start: 0.7694 (mmp) cc_final: 0.6927 (mtm) REVERT: A 1097 TYR cc_start: 0.7743 (t80) cc_final: 0.7364 (t80) REVERT: A 1136 LEU cc_start: 0.9481 (mt) cc_final: 0.9080 (tp) REVERT: A 1141 MET cc_start: 0.8918 (mtm) cc_final: 0.8712 (mtt) REVERT: A 1147 ASP cc_start: 0.9198 (m-30) cc_final: 0.8970 (m-30) REVERT: A 1210 LEU cc_start: 0.8152 (mm) cc_final: 0.7923 (mm) REVERT: A 1279 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8981 (pp30) REVERT: A 1375 ILE cc_start: 0.9090 (mm) cc_final: 0.8814 (mm) REVERT: A 1680 TRP cc_start: 0.9076 (t-100) cc_final: 0.8375 (t-100) REVERT: A 1773 LEU cc_start: 0.8914 (tt) cc_final: 0.8653 (tt) REVERT: A 1782 MET cc_start: 0.9157 (mtm) cc_final: 0.8916 (mtt) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.1040 time to fit residues: 26.3449 Evaluate side-chains 137 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1231 HIS A1713 GLN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063187 restraints weight = 60712.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064748 restraints weight = 43307.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065905 restraints weight = 33765.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066698 restraints weight = 28001.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067177 restraints weight = 24466.710| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13009 Z= 0.181 Angle : 0.715 11.802 17579 Z= 0.358 Chirality : 0.045 0.197 2031 Planarity : 0.004 0.040 2196 Dihedral : 8.156 88.573 1806 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.21), residues: 1558 helix: 0.55 (0.18), residues: 794 sheet: -0.44 (0.50), residues: 92 loop : -2.20 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 614 TYR 0.017 0.002 TYR A 296 PHE 0.021 0.002 PHE A 852 TRP 0.037 0.002 TRP A 116 HIS 0.010 0.001 HIS A 910 Details of bonding type rmsd covalent geometry : bond 0.00390 (13003) covalent geometry : angle 0.71211 (17572) SS BOND : bond 0.00381 ( 2) SS BOND : angle 1.94153 ( 4) hydrogen bonds : bond 0.03534 ( 590) hydrogen bonds : angle 4.45784 ( 1704) metal coordination : bond 0.00929 ( 4) metal coordination : angle 4.82383 ( 3) ********************** 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 168 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9513 (m-80) cc_final: 0.9160 (m-80) REVERT: A 478 MET cc_start: 0.7635 (mtt) cc_final: 0.7046 (mtt) REVERT: A 565 MET cc_start: 0.8562 (tpt) cc_final: 0.8346 (tpp) REVERT: A 695 TYR cc_start: 0.9301 (t80) cc_final: 0.8779 (t80) REVERT: A 702 LEU cc_start: 0.9447 (mt) cc_final: 0.9024 (mt) REVERT: A 708 LYS cc_start: 0.9102 (pttp) cc_final: 0.8296 (ptmm) REVERT: A 850 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8205 (mt-10) REVERT: A 851 ARG cc_start: 0.8596 (ptt180) cc_final: 0.8103 (ptt90) REVERT: A 910 HIS cc_start: 0.8313 (m-70) cc_final: 0.8075 (m170) REVERT: A 1026 MET cc_start: 0.7660 (mmp) cc_final: 0.6964 (mtm) REVERT: A 1097 TYR cc_start: 0.8091 (t80) cc_final: 0.7763 (t80) REVERT: A 1136 LEU cc_start: 0.9484 (mt) cc_final: 0.9090 (tp) REVERT: A 1141 MET cc_start: 0.8944 (mtm) cc_final: 0.8680 (mtt) REVERT: A 1147 ASP cc_start: 0.9178 (m-30) cc_final: 0.8974 (m-30) REVERT: A 1210 LEU cc_start: 0.8201 (mm) cc_final: 0.7969 (mm) REVERT: A 1375 ILE cc_start: 0.9264 (mm) cc_final: 0.8963 (mm) REVERT: A 1680 TRP cc_start: 0.9139 (t-100) cc_final: 0.8527 (t-100) REVERT: A 1773 LEU cc_start: 0.8929 (tt) cc_final: 0.8616 (tt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1004 time to fit residues: 25.5671 Evaluate side-chains 130 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 37 optimal weight: 0.0670 chunk 94 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 189 HIS ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1231 HIS A1405 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.064775 restraints weight = 58975.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066405 restraints weight = 42125.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.067509 restraints weight = 32858.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068373 restraints weight = 27260.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068946 restraints weight = 23703.931| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13009 Z= 0.126 Angle : 0.688 12.007 17579 Z= 0.341 Chirality : 0.043 0.187 2031 Planarity : 0.004 0.054 2196 Dihedral : 8.054 88.058 1806 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1558 helix: 0.61 (0.18), residues: 794 sheet: -0.25 (0.53), residues: 84 loop : -2.18 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.015 0.001 TYR A 296 PHE 0.027 0.001 PHE A 852 TRP 0.032 0.002 TRP A 116 HIS 0.010 0.001 HIS A 910 Details of bonding type rmsd covalent geometry : bond 0.00276 (13003) covalent geometry : angle 0.68507 (17572) SS BOND : bond 0.00354 ( 2) SS BOND : angle 1.58395 ( 4) hydrogen bonds : bond 0.03347 ( 590) hydrogen bonds : angle 4.32118 ( 1704) metal coordination : bond 0.01603 ( 4) metal coordination : angle 4.29000 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.79 seconds wall clock time: 32 minutes 52.50 seconds (1972.50 seconds total)