Starting phenix.real_space_refine on Sat Sep 12 02:40:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kle_0709/09_2026/6kle_0709.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kle_0709/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6kle_0709/09_2026/6kle_0709.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kle_0709/09_2026/6kle_0709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kle_0709/09_2026/6kle_0709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kle_0709/09_2026/6kle_0709.map" model { file = "/net/cci-nas-00/data/ceres_data/6kle_0709/09_2026/6kle_0709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kle_0709/09_2026/6kle_0709.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.85, 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: 1.12 Conformation dependent library (CDL) restraints added in 617.6 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: 0.44 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: 2.09 Time building geometry restraints manager: 1.54 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: 17218 2.13 - 4.26: 302 4.26 - 6.40: 45 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 - 17.50: 7113 17.50 - 35.01: 625 35.01 - 52.51: 102 52.51 - 70.01: 32 70.01 - 87.52: 19 Dihedral angle restraints: 7891 sinusoidal: 3236 harmonic: 4655 Sorted by residual: dihedral pdb=" C4' U B 16 " pdb=" C3' U B 16 " pdb=" C2' U B 16 " pdb=" C1' U B 16 " ideal model delta sinusoidal sigma weight residual 36.34 -35.58 71.92 1 3.10e+00 1.04e-01 6.89e+02 dihedral pdb=" C4' U B 14 " pdb=" C3' U B 14 " pdb=" C2' U B 14 " pdb=" C1' U B 14 " ideal model delta sinusoidal sigma weight residual 36.34 -35.15 71.50 1 3.10e+00 1.04e-01 6.82e+02 dihedral pdb=" C4' C B 13 " pdb=" C3' C B 13 " pdb=" C2' C B 13 " pdb=" C1' C B 13 " ideal model delta sinusoidal sigma weight residual 36.34 -34.73 71.08 1 3.10e+00 1.04e-01 6.75e+02 ... (remaining 7888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1648 0.055 - 0.111: 330 0.111 - 0.166: 33 0.166 - 0.221: 11 0.221 - 0.277: 9 Chirality restraints: 2031 Sorted by residual: chirality pdb=" C2' U B 16 " pdb=" C3' U B 16 " pdb=" O2' U B 16 " pdb=" C1' U B 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2' U B 14 " pdb=" C3' U B 14 " pdb=" O2' U B 14 " pdb=" C1' U B 14 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2' C B 13 " pdb=" C3' C B 13 " pdb=" O2' C B 13 " pdb=" C1' C B 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (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: 0.600 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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= 0.138 Angle : 0.679 10.660 17579 Z= 0.344 Chirality : 0.048 0.277 2031 Planarity : 0.004 0.041 2196 Dihedral : 14.220 87.518 4851 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/Z covalent geometry : bond 0.00271 / 0.13 (13003) covalent geometry : angle 0.67399 / 0.34 (17572) SS BOND : bond 0.00218 / 0.11 ( 2) SS BOND : angle 1.08416 / 0.61 ( 4) hydrogen bonds : bond 0.12647 / 8.93 ( 590) hydrogen bonds : angle 5.38216 / 3.79 ( 1704) metal coordination : bond 0.06855 / 3.43 ( 4) metal coordination : angle 5.95700 / 4.75 ( 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 : 0.338 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: 0.0954 time to fit residues: 29.0079 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 : 0.361 ------------------------------------------------------------------------------- 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... ** 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 ** 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 = 0.3681 r_free = 0.3681 target = 0.088545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065440 restraints weight = 58311.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067026 restraints weight = 42815.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068191 restraints weight = 33746.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.069015 restraints weight = 28197.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069642 restraints weight = 24619.253| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13009 Z= 0.190 Angle : 0.745 16.678 17579 Z= 0.355 Chirality : 0.054 0.815 2031 Planarity : 0.004 0.048 2196 Dihedral : 6.876 73.415 1772 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.14 % Allowed : 8.37 % Favored : 91.49 % 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: -0.81 (0.21), residues: 1558 helix: 0.75 (0.19), residues: 795 sheet: 0.22 (0.55), residues: 74 loop : -2.25 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 851 TYR 0.018 0.002 TYR A 558 PHE 0.039 0.001 PHE A 22 TRP 0.024 0.002 TRP A1680 HIS 0.008 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (13003) covalent geometry : angle 0.74306 / 0.35 (17572) SS BOND : bond 0.00326 / 0.16 ( 2) SS BOND : angle 1.27306 / 0.73 ( 4) hydrogen bonds : bond 0.03901 / 2.71 ( 590) hydrogen bonds : angle 4.38957 / 3.09 ( 1704) metal coordination : bond 0.00988 / 0.49 ( 4) metal coordination : angle 4.21731 / 3.10 ( 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 186 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.393 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: 0.9512 (m-80) cc_final: 0.9136 (m-80) REVERT: A 51 GLU cc_start: 0.7924 (pp20) cc_final: 0.7325 (tm-30) REVERT: A 387 MET cc_start: 0.8640 (pmm) cc_final: 0.8421 (pmm) REVERT: A 478 MET cc_start: 0.7858 (mtt) cc_final: 0.7488 (mtt) REVERT: A 695 TYR cc_start: 0.9424 (t80) cc_final: 0.9000 (t80) REVERT: A 699 VAL cc_start: 0.9449 (t) cc_final: 0.9244 (t) REVERT: A 702 LEU cc_start: 0.9390 (mt) cc_final: 0.8983 (mt) REVERT: A 708 LYS cc_start: 0.8939 (pttp) cc_final: 0.8323 (ptmm) REVERT: A 836 ASP cc_start: 0.8327 (t0) cc_final: 0.8054 (t0) REVERT: A 848 MET cc_start: 0.8546 (mmp) cc_final: 0.8291 (mmp) REVERT: A 851 ARG cc_start: 0.8952 (ptt180) cc_final: 0.8698 (ptt180) REVERT: A 1027 CYS cc_start: 0.7881 (t) cc_final: 0.7616 (t) REVERT: A 1141 MET cc_start: 0.9087 (mtm) cc_final: 0.8765 (mtt) REVERT: A 1147 ASP cc_start: 0.9209 (m-30) cc_final: 0.8987 (m-30) REVERT: A 1210 LEU cc_start: 0.8461 (mm) cc_final: 0.8261 (mm) REVERT: A 1274 MET cc_start: 0.9057 (ttm) cc_final: 0.8765 (ttt) REVERT: A 1375 ILE cc_start: 0.8985 (mm) cc_final: 0.8729 (mm) REVERT: A 1678 ILE cc_start: 0.8950 (tp) cc_final: 0.8581 (tp) REVERT: A 1733 MET cc_start: 0.3577 (tpt) cc_final: 0.2905 (tpt) REVERT: A 1773 LEU cc_start: 0.8872 (tt) cc_final: 0.8572 (tt) outliers start: 2 outliers final: 0 residues processed: 186 average time/residue: 0.0992 time to fit residues: 27.5820 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 : 0.378 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 120 optimal weight: 0.0870 chunk 5 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3713 r_free = 0.3713 target = 0.090156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066333 restraints weight = 58719.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068227 restraints weight = 40658.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.069561 restraints weight = 30907.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070523 restraints weight = 25155.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071188 restraints weight = 21683.136| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13009 Z= 0.115 Angle : 0.664 11.478 17579 Z= 0.320 Chirality : 0.048 0.457 2031 Planarity : 0.003 0.041 2196 Dihedral : 6.654 70.490 1772 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: 0.81 (0.19), residues: 792 sheet: 0.45 (0.56), residues: 74 loop : -2.29 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 614 TYR 0.015 0.001 TYR A 296 PHE 0.028 0.001 PHE A 22 TRP 0.018 0.001 TRP A 116 HIS 0.011 0.001 HIS A 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (13003) covalent geometry : angle 0.66233 / 0.32 (17572) SS BOND : bond 0.00460 / 0.23 ( 2) SS BOND : angle 0.81202 / 0.50 ( 4) hydrogen bonds : bond 0.03363 / 2.34 ( 590) hydrogen bonds : angle 4.05024 / 2.85 ( 1704) metal coordination : bond 0.01387 / 0.69 ( 4) metal coordination : angle 3.79448 / 2.75 ( 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 188 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.389 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: 0.9474 (m-80) cc_final: 0.9122 (m-80) REVERT: A 387 MET cc_start: 0.8642 (pmm) cc_final: 0.8399 (pmm) REVERT: A 394 LEU cc_start: 0.9026 (tp) cc_final: 0.8781 (tt) REVERT: A 620 ILE cc_start: 0.9423 (mt) cc_final: 0.9201 (mt) REVERT: A 695 TYR cc_start: 0.9276 (t80) cc_final: 0.9041 (t80) REVERT: A 702 LEU cc_start: 0.9455 (mt) cc_final: 0.9033 (mt) REVERT: A 708 LYS cc_start: 0.8970 (pttp) cc_final: 0.8407 (ptmm) REVERT: A 848 MET cc_start: 0.8563 (mmp) cc_final: 0.8315 (mmp) REVERT: A 851 ARG cc_start: 0.8961 (ptt180) cc_final: 0.8760 (ptt180) REVERT: A 1027 CYS cc_start: 0.7859 (t) cc_final: 0.7589 (t) REVERT: A 1097 TYR cc_start: 0.7737 (t80) cc_final: 0.7489 (t80) REVERT: A 1136 LEU cc_start: 0.9408 (mt) cc_final: 0.8916 (tp) REVERT: A 1141 MET cc_start: 0.9010 (mtm) cc_final: 0.8722 (mtt) REVERT: A 1147 ASP cc_start: 0.9159 (m-30) cc_final: 0.8913 (m-30) REVERT: A 1210 LEU cc_start: 0.8360 (mm) cc_final: 0.8148 (mm) REVERT: A 1274 MET cc_start: 0.8987 (ttm) cc_final: 0.8652 (ttt) REVERT: A 1678 ILE cc_start: 0.9003 (tp) cc_final: 0.8602 (tp) REVERT: A 1680 TRP cc_start: 0.8673 (t-100) cc_final: 0.7982 (t-100) REVERT: A 1681 ASP cc_start: 0.9165 (m-30) cc_final: 0.8950 (m-30) REVERT: A 1773 LEU cc_start: 0.8784 (tt) cc_final: 0.8403 (tt) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0895 time to fit residues: 25.9358 Evaluate side-chains 149 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 30.0000 chunk 21 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS A1405 HIS A1665 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 = 0.3675 r_free = 0.3675 target = 0.088009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065146 restraints weight = 58370.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066794 restraints weight = 41929.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067947 restraints weight = 32691.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068822 restraints weight = 27035.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069357 restraints weight = 23562.987| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2010 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= 0.153 Angle : 0.656 9.733 17579 Z= 0.325 Chirality : 0.046 0.338 2031 Planarity : 0.004 0.044 2196 Dihedral : 6.671 75.239 1772 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.18), residues: 792 sheet: 0.20 (0.56), residues: 74 loop : -2.29 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 614 TYR 0.015 0.001 TYR A 296 PHE 0.033 0.001 PHE A1683 TRP 0.019 0.002 TRP A 116 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (13003) covalent geometry : angle 0.65381 / 0.32 (17572) SS BOND : bond 0.00308 / 0.15 ( 2) SS BOND : angle 1.28511 / 0.73 ( 4) hydrogen bonds : bond 0.03344 / 2.33 ( 590) hydrogen bonds : angle 4.16928 / 2.93 ( 1704) metal coordination : bond 0.00765 / 0.38 ( 4) metal coordination : angle 4.23055 / 2.94 ( 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 180 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.478 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: 0.9517 (m-80) cc_final: 0.9145 (m-80) REVERT: A 51 GLU cc_start: 0.7892 (pp20) cc_final: 0.7284 (tm-30) REVERT: A 387 MET cc_start: 0.8475 (pmm) cc_final: 0.8156 (pmm) REVERT: A 695 TYR cc_start: 0.9442 (t80) cc_final: 0.8927 (t80) REVERT: A 702 LEU cc_start: 0.9362 (mt) cc_final: 0.8913 (mt) REVERT: A 708 LYS cc_start: 0.9006 (pttp) cc_final: 0.8372 (ptmm) REVERT: A 1027 CYS cc_start: 0.7930 (t) cc_final: 0.7679 (t) REVERT: A 1116 LYS cc_start: 0.8307 (tptt) cc_final: 0.8000 (tptt) REVERT: A 1136 LEU cc_start: 0.9357 (mt) cc_final: 0.9002 (tp) REVERT: A 1141 MET cc_start: 0.9072 (mtm) cc_final: 0.8810 (mtt) REVERT: A 1147 ASP cc_start: 0.9206 (m-30) cc_final: 0.8972 (m-30) REVERT: A 1210 LEU cc_start: 0.8480 (mm) cc_final: 0.8231 (mm) REVERT: A 1375 ILE cc_start: 0.8952 (mm) cc_final: 0.8630 (mm) REVERT: A 1680 TRP cc_start: 0.8925 (t-100) cc_final: 0.8258 (t-100) REVERT: A 1773 LEU cc_start: 0.8885 (tt) cc_final: 0.8539 (tt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0964 time to fit residues: 26.1965 Evaluate side-chains 136 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS A1405 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.088982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065610 restraints weight = 59455.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067460 restraints weight = 40949.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.068745 restraints weight = 31152.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069632 restraints weight = 25481.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.070329 restraints weight = 22051.604| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13009 Z= 0.115 Angle : 0.646 9.610 17579 Z= 0.315 Chirality : 0.045 0.287 2031 Planarity : 0.003 0.037 2196 Dihedral : 6.606 77.457 1772 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % 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: 0.79 (0.18), residues: 795 sheet: 0.20 (0.57), residues: 74 loop : -2.29 (0.23), residues: 689 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 0.045 0.001 PHE A 22 TRP 0.016 0.001 TRP A 116 HIS 0.006 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (13003) covalent geometry : angle 0.64454 / 0.32 (17572) SS BOND : bond 0.00320 / 0.16 ( 2) SS BOND : angle 0.81177 / 0.48 ( 4) hydrogen bonds : bond 0.03122 / 2.19 ( 590) hydrogen bonds : angle 4.03580 / 2.86 ( 1704) metal coordination : bond 0.01552 / 0.78 ( 4) metal coordination : angle 3.83121 / 2.79 ( 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 182 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.341 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: 0.9492 (m-80) cc_final: 0.9114 (m-80) REVERT: A 387 MET cc_start: 0.8430 (pmm) cc_final: 0.8029 (pmm) REVERT: A 478 MET cc_start: 0.7665 (mtt) cc_final: 0.7304 (mtt) REVERT: A 620 ILE cc_start: 0.9398 (mt) cc_final: 0.9181 (mt) REVERT: A 695 TYR cc_start: 0.9326 (t80) cc_final: 0.8716 (t80) REVERT: A 699 VAL cc_start: 0.9457 (t) cc_final: 0.9250 (t) REVERT: A 702 LEU cc_start: 0.9427 (mt) cc_final: 0.8964 (mt) REVERT: A 708 LYS cc_start: 0.8977 (pttp) cc_final: 0.8457 (ptmm) REVERT: A 848 MET cc_start: 0.8628 (mmp) cc_final: 0.8371 (mmm) REVERT: A 851 ARG cc_start: 0.9150 (ptt180) cc_final: 0.8874 (ptt180) REVERT: A 1027 CYS cc_start: 0.7909 (t) cc_final: 0.7651 (t) REVERT: A 1097 TYR cc_start: 0.7917 (t80) cc_final: 0.7521 (t80) REVERT: A 1116 LYS cc_start: 0.8265 (tptt) cc_final: 0.7971 (tptt) REVERT: A 1136 LEU cc_start: 0.9398 (mt) cc_final: 0.8928 (tp) REVERT: A 1141 MET cc_start: 0.8968 (mtm) cc_final: 0.8712 (mtt) REVERT: A 1147 ASP cc_start: 0.9260 (m-30) cc_final: 0.8815 (m-30) REVERT: A 1174 MET cc_start: 0.8707 (ptp) cc_final: 0.8503 (ptt) REVERT: A 1210 LEU cc_start: 0.8306 (mm) cc_final: 0.8097 (mm) REVERT: A 1304 LEU cc_start: 0.9284 (tt) cc_final: 0.8826 (tt) REVERT: A 1487 ASP cc_start: 0.6817 (t0) cc_final: 0.6423 (t0) REVERT: A 1680 TRP cc_start: 0.8767 (t-100) cc_final: 0.8208 (t-100) REVERT: A 1773 LEU cc_start: 0.8755 (tt) cc_final: 0.8484 (tt) REVERT: A 1782 MET cc_start: 0.8984 (mtp) cc_final: 0.8778 (mtt) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.1006 time to fit residues: 27.5459 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 : 0.439 ------------------------------------------------------------------------------- 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: 0.2980 chunk 10 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** 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 = 0.3659 r_free = 0.3659 target = 0.087058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064317 restraints weight = 58851.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065897 restraints weight = 42698.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067101 restraints weight = 33373.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067931 restraints weight = 27693.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.068493 restraints weight = 24146.468| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13009 Z= 0.163 Angle : 0.674 9.844 17579 Z= 0.335 Chirality : 0.045 0.264 2031 Planarity : 0.004 0.040 2196 Dihedral : 6.661 80.707 1772 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: -0.88 (0.21), residues: 1558 helix: 0.68 (0.18), residues: 798 sheet: 0.21 (0.56), residues: 74 loop : -2.28 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 376 TYR 0.015 0.001 TYR A 296 PHE 0.028 0.001 PHE A 852 TRP 0.020 0.002 TRP A 116 HIS 0.006 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (13003) covalent geometry : angle 0.67121 / 0.33 (17572) SS BOND : bond 0.00495 / 0.25 ( 2) SS BOND : angle 2.03791 / 1.19 ( 4) hydrogen bonds : bond 0.03291 / 2.31 ( 590) hydrogen bonds : angle 4.21464 / 2.98 ( 1704) metal coordination : bond 0.00549 / 0.27 ( 4) metal coordination : angle 4.37306 / 3.05 ( 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 174 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9509 (m-80) cc_final: 0.9123 (m-80) REVERT: A 51 GLU cc_start: 0.7967 (pp20) cc_final: 0.7324 (tm-30) REVERT: A 387 MET cc_start: 0.8371 (pmm) cc_final: 0.8127 (pmm) REVERT: A 478 MET cc_start: 0.7733 (mtt) cc_final: 0.7398 (mtt) REVERT: A 595 MET cc_start: 0.8908 (tpt) cc_final: 0.8658 (tpp) REVERT: A 695 TYR cc_start: 0.9309 (t80) cc_final: 0.8842 (t80) REVERT: A 702 LEU cc_start: 0.9382 (mt) cc_final: 0.8927 (mt) REVERT: A 708 LYS cc_start: 0.9068 (pttp) cc_final: 0.8496 (ptmm) REVERT: A 722 GLU cc_start: 0.8884 (pt0) cc_final: 0.8218 (pt0) REVERT: A 848 MET cc_start: 0.8403 (mmp) cc_final: 0.7904 (mmm) REVERT: A 850 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8122 (pt0) REVERT: A 851 ARG cc_start: 0.9144 (ptt180) cc_final: 0.8696 (ptt180) REVERT: A 1027 CYS cc_start: 0.7951 (t) cc_final: 0.7640 (t) REVERT: A 1116 LYS cc_start: 0.8355 (tptt) cc_final: 0.8062 (tptt) REVERT: A 1136 LEU cc_start: 0.9362 (mt) cc_final: 0.8995 (tp) REVERT: A 1141 MET cc_start: 0.9020 (mtm) cc_final: 0.8762 (mtt) REVERT: A 1147 ASP cc_start: 0.9215 (m-30) cc_final: 0.8960 (m-30) REVERT: A 1210 LEU cc_start: 0.8261 (mm) cc_final: 0.7999 (mm) REVERT: A 1279 GLN cc_start: 0.9252 (tp-100) cc_final: 0.8916 (pp30) REVERT: A 1375 ILE cc_start: 0.9033 (mm) cc_final: 0.8809 (mm) REVERT: A 1680 TRP cc_start: 0.9065 (t-100) cc_final: 0.8323 (t-100) REVERT: A 1773 LEU cc_start: 0.8789 (tt) cc_final: 0.8509 (tt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0984 time to fit residues: 25.7001 Evaluate side-chains 131 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 0.9980 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 141 optimal weight: 0.0040 chunk 122 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 629 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.088502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065008 restraints weight = 58705.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066827 restraints weight = 41272.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068096 restraints weight = 31484.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.069034 restraints weight = 25827.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069658 restraints weight = 22287.266| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13009 Z= 0.117 Angle : 0.660 9.996 17579 Z= 0.320 Chirality : 0.044 0.227 2031 Planarity : 0.003 0.042 2196 Dihedral : 6.489 82.021 1772 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.07 % Allowed : 1.81 % Favored : 98.12 % 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: -0.81 (0.21), residues: 1558 helix: 0.73 (0.18), residues: 796 sheet: 0.30 (0.56), residues: 74 loop : -2.24 (0.23), residues: 688 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 0.030 0.001 PHE A 852 TRP 0.017 0.001 TRP A 116 HIS 0.004 0.001 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (13003) covalent geometry : angle 0.65801 / 0.32 (17572) SS BOND : bond 0.00395 / 0.20 ( 2) SS BOND : angle 1.30309 / 0.77 ( 4) hydrogen bonds : bond 0.03089 / 2.16 ( 590) hydrogen bonds : angle 4.10167 / 2.90 ( 1704) metal coordination : bond 0.01433 / 0.72 ( 4) metal coordination : angle 4.03268 / 2.84 ( 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 177 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9498 (m-80) cc_final: 0.9115 (m-80) REVERT: A 51 GLU cc_start: 0.7929 (pp20) cc_final: 0.7320 (tm-30) REVERT: A 478 MET cc_start: 0.7570 (mtt) cc_final: 0.7194 (mtt) REVERT: A 695 TYR cc_start: 0.9263 (t80) cc_final: 0.8847 (t80) REVERT: A 702 LEU cc_start: 0.9430 (mt) cc_final: 0.8984 (mt) REVERT: A 708 LYS cc_start: 0.8851 (pttp) cc_final: 0.8265 (ptmm) REVERT: A 848 MET cc_start: 0.8326 (mmp) cc_final: 0.7762 (mmm) REVERT: A 850 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8047 (pt0) REVERT: A 851 ARG cc_start: 0.8998 (ptt180) cc_final: 0.8512 (ptt180) REVERT: A 910 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7635 (m170) REVERT: A 1026 MET cc_start: 0.7733 (mmt) cc_final: 0.7077 (mtm) REVERT: A 1116 LYS cc_start: 0.8322 (tptt) cc_final: 0.7922 (mmtt) REVERT: A 1136 LEU cc_start: 0.9445 (mt) cc_final: 0.9019 (tp) REVERT: A 1141 MET cc_start: 0.8971 (mtm) cc_final: 0.8725 (mtt) REVERT: A 1143 ARG cc_start: 0.8741 (ptm160) cc_final: 0.8495 (ptm160) REVERT: A 1147 ASP cc_start: 0.9148 (m-30) cc_final: 0.8891 (m-30) REVERT: A 1210 LEU cc_start: 0.8219 (mm) cc_final: 0.7973 (mm) REVERT: A 1279 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8631 (pp30) REVERT: A 1375 ILE cc_start: 0.8873 (mm) cc_final: 0.8577 (mm) REVERT: A 1680 TRP cc_start: 0.9029 (t-100) cc_final: 0.8390 (t-100) REVERT: A 1773 LEU cc_start: 0.8836 (tt) cc_final: 0.8542 (tt) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.0936 time to fit residues: 25.0395 Evaluate side-chains 134 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 1.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 141 optimal weight: 0.0980 chunk 140 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 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 = 0.3698 r_free = 0.3698 target = 0.089087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066261 restraints weight = 57011.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067932 restraints weight = 40978.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069128 restraints weight = 31922.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069911 restraints weight = 26466.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070566 restraints weight = 23108.666| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13009 Z= 0.110 Angle : 0.651 10.924 17579 Z= 0.314 Chirality : 0.043 0.208 2031 Planarity : 0.003 0.037 2196 Dihedral : 6.334 83.585 1772 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -0.78 (0.21), residues: 1558 helix: 0.71 (0.18), residues: 795 sheet: 0.35 (0.56), residues: 74 loop : -2.16 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 614 TYR 0.014 0.001 TYR A 296 PHE 0.027 0.001 PHE A 852 TRP 0.016 0.001 TRP A 116 HIS 0.008 0.001 HIS A 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (13003) covalent geometry : angle 0.64897 / 0.31 (17572) SS BOND : bond 0.00414 / 0.21 ( 2) SS BOND : angle 1.15934 / 0.70 ( 4) hydrogen bonds : bond 0.03026 / 2.10 ( 590) hydrogen bonds : angle 4.05896 / 2.86 ( 1704) metal coordination : bond 0.01674 / 0.84 ( 4) metal coordination : angle 3.75879 / 2.70 ( 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 180 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.9481 (m-80) cc_final: 0.9109 (m-80) REVERT: A 51 GLU cc_start: 0.7862 (pp20) cc_final: 0.7259 (tm-30) REVERT: A 338 LYS cc_start: 0.9519 (pptt) cc_final: 0.9173 (pptt) REVERT: A 478 MET cc_start: 0.7556 (mtt) cc_final: 0.7198 (mtt) REVERT: A 557 VAL cc_start: 0.9301 (t) cc_final: 0.9023 (p) REVERT: A 695 TYR cc_start: 0.9271 (t80) cc_final: 0.9015 (t80) REVERT: A 702 LEU cc_start: 0.9404 (mt) cc_final: 0.8900 (mt) REVERT: A 708 LYS cc_start: 0.8777 (pttp) cc_final: 0.7803 (ptmm) REVERT: A 850 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8040 (pt0) REVERT: A 910 HIS cc_start: 0.8353 (m-70) cc_final: 0.8072 (m170) REVERT: A 1026 MET cc_start: 0.7584 (mmt) cc_final: 0.6710 (mtm) REVERT: A 1116 LYS cc_start: 0.8352 (tptt) cc_final: 0.7808 (mmtt) REVERT: A 1136 LEU cc_start: 0.9443 (mt) cc_final: 0.8996 (tp) REVERT: A 1141 MET cc_start: 0.9003 (mtm) cc_final: 0.8752 (mtt) REVERT: A 1147 ASP cc_start: 0.9161 (m-30) cc_final: 0.8941 (m-30) REVERT: A 1154 ASN cc_start: 0.7987 (m110) cc_final: 0.7760 (m110) REVERT: A 1210 LEU cc_start: 0.8158 (mm) cc_final: 0.7939 (mm) REVERT: A 1279 GLN cc_start: 0.9225 (tp-100) cc_final: 0.8589 (pp30) REVERT: A 1375 ILE cc_start: 0.8877 (mm) cc_final: 0.8635 (mm) REVERT: A 1487 ASP cc_start: 0.7009 (t0) cc_final: 0.6508 (t0) REVERT: A 1680 TRP cc_start: 0.9071 (t-100) cc_final: 0.8350 (t-100) REVERT: A 1773 LEU cc_start: 0.8871 (tt) cc_final: 0.8621 (tt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1028 time to fit residues: 28.4441 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 : 0.587 ------------------------------------------------------------------------------- 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: 0.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 145 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN A1231 HIS A1405 HIS A1689 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 = 0.3683 r_free = 0.3683 target = 0.088396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065615 restraints weight = 58257.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067260 restraints weight = 41959.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068382 restraints weight = 32791.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.069283 restraints weight = 27276.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069915 restraints weight = 23649.751| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13009 Z= 0.125 Angle : 0.677 11.270 17579 Z= 0.329 Chirality : 0.044 0.206 2031 Planarity : 0.003 0.037 2196 Dihedral : 6.312 84.372 1772 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.07 % Allowed : 0.77 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.67 (0.18), residues: 795 sheet: 0.45 (0.55), residues: 76 loop : -2.16 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 19 TYR 0.015 0.001 TYR A 296 PHE 0.034 0.001 PHE A1357 TRP 0.023 0.001 TRP A 598 HIS 0.009 0.001 HIS A 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13003) covalent geometry : angle 0.67467 / 0.33 (17572) SS BOND : bond 0.00425 / 0.21 ( 2) SS BOND : angle 1.80305 / 1.04 ( 4) hydrogen bonds : bond 0.03182 / 2.21 ( 590) hydrogen bonds : angle 4.13250 / 2.94 ( 1704) metal coordination : bond 0.01454 / 0.73 ( 4) metal coordination : angle 4.01554 / 2.89 ( 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 171 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.553 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: 0.9471 (m-80) cc_final: 0.9091 (m-80) REVERT: A 338 LYS cc_start: 0.9514 (pptt) cc_final: 0.9173 (pptt) REVERT: A 620 ILE cc_start: 0.9368 (mt) cc_final: 0.9122 (mt) REVERT: A 702 LEU cc_start: 0.9422 (mt) cc_final: 0.8902 (mt) REVERT: A 708 LYS cc_start: 0.8813 (pttp) cc_final: 0.7905 (ptmm) REVERT: A 848 MET cc_start: 0.8387 (mmp) cc_final: 0.8070 (mmm) REVERT: A 850 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7969 (pt0) REVERT: A 851 ARG cc_start: 0.8886 (ptt180) cc_final: 0.8267 (ptt180) REVERT: A 910 HIS cc_start: 0.8282 (m-70) cc_final: 0.7956 (m170) REVERT: A 1026 MET cc_start: 0.7554 (mmt) cc_final: 0.6622 (mtm) REVERT: A 1116 LYS cc_start: 0.8344 (tptt) cc_final: 0.7790 (mmtt) REVERT: A 1136 LEU cc_start: 0.9449 (mt) cc_final: 0.8919 (tp) REVERT: A 1141 MET cc_start: 0.8918 (mtm) cc_final: 0.8699 (mtt) REVERT: A 1147 ASP cc_start: 0.9132 (m-30) cc_final: 0.8929 (m-30) REVERT: A 1210 LEU cc_start: 0.8037 (mm) cc_final: 0.7833 (mm) REVERT: A 1274 MET cc_start: 0.8731 (ttt) cc_final: 0.8236 (tpp) REVERT: A 1279 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8596 (pp30) REVERT: A 1375 ILE cc_start: 0.8828 (mm) cc_final: 0.8572 (mm) REVERT: A 1487 ASP cc_start: 0.6973 (t0) cc_final: 0.6457 (t0) REVERT: A 1680 TRP cc_start: 0.9064 (t-100) cc_final: 0.8361 (t-100) REVERT: A 1773 LEU cc_start: 0.8859 (tt) cc_final: 0.8596 (tt) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1104 time to fit residues: 28.5738 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 : 0.521 ------------------------------------------------------------------------------- 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: 9.9990 chunk 149 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1231 HIS A1689 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 = 0.3691 r_free = 0.3691 target = 0.088822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065915 restraints weight = 58441.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067556 restraints weight = 42014.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068748 restraints weight = 32826.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069586 restraints weight = 27257.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.070110 restraints weight = 23729.091| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13009 Z= 0.118 Angle : 0.670 11.669 17579 Z= 0.325 Chirality : 0.044 0.206 2031 Planarity : 0.003 0.037 2196 Dihedral : 6.221 84.668 1772 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.82 (0.21), residues: 1558 helix: 0.62 (0.18), residues: 795 sheet: 0.34 (0.56), residues: 77 loop : -2.13 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.014 0.001 TYR A 296 PHE 0.022 0.001 PHE A 22 TRP 0.030 0.001 TRP A 116 HIS 0.011 0.001 HIS A 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (13003) covalent geometry : angle 0.66730 / 0.32 (17572) SS BOND : bond 0.00401 / 0.20 ( 2) SS BOND : angle 1.55842 / 0.93 ( 4) hydrogen bonds : bond 0.03128 / 2.16 ( 590) hydrogen bonds : angle 4.13084 / 2.94 ( 1704) metal coordination : bond 0.01609 / 0.81 ( 4) metal coordination : angle 3.94785 / 2.91 ( 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 174 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.531 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: 0.9476 (m-80) cc_final: 0.9107 (m-80) REVERT: A 51 GLU cc_start: 0.7830 (pp20) cc_final: 0.7213 (tm-30) REVERT: A 338 LYS cc_start: 0.9522 (pptt) cc_final: 0.9160 (pptt) REVERT: A 352 PHE cc_start: 0.9280 (t80) cc_final: 0.8950 (t80) REVERT: A 478 MET cc_start: 0.7755 (mtt) cc_final: 0.7218 (mtt) REVERT: A 565 MET cc_start: 0.8230 (tpt) cc_final: 0.7975 (tpp) REVERT: A 635 LEU cc_start: 0.9506 (mm) cc_final: 0.9272 (mm) REVERT: A 695 TYR cc_start: 0.9304 (t80) cc_final: 0.9051 (t80) REVERT: A 702 LEU cc_start: 0.9408 (mt) cc_final: 0.8935 (mt) REVERT: A 708 LYS cc_start: 0.8750 (pttp) cc_final: 0.7787 (ptmm) REVERT: A 848 MET cc_start: 0.8406 (mmp) cc_final: 0.8068 (mmm) REVERT: A 850 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7949 (pt0) REVERT: A 851 ARG cc_start: 0.8910 (ptt180) cc_final: 0.8271 (ptt180) REVERT: A 910 HIS cc_start: 0.8241 (m-70) cc_final: 0.7893 (m170) REVERT: A 1026 MET cc_start: 0.7540 (mmt) cc_final: 0.6721 (mtm) REVERT: A 1136 LEU cc_start: 0.9421 (mt) cc_final: 0.8892 (tp) REVERT: A 1141 MET cc_start: 0.8942 (mtm) cc_final: 0.8700 (mtt) REVERT: A 1210 LEU cc_start: 0.8127 (mm) cc_final: 0.7913 (mm) REVERT: A 1274 MET cc_start: 0.8674 (ttt) cc_final: 0.8249 (tpp) REVERT: A 1279 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8597 (pp30) REVERT: A 1375 ILE cc_start: 0.8956 (mm) cc_final: 0.8692 (mm) REVERT: A 1487 ASP cc_start: 0.6969 (t0) cc_final: 0.6478 (t0) REVERT: A 1530 PHE cc_start: 0.8204 (m-10) cc_final: 0.7875 (m-10) REVERT: A 1773 LEU cc_start: 0.8891 (tt) cc_final: 0.8624 (tt) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1108 time to fit residues: 28.8771 Evaluate side-chains 133 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.0050 chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.088579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065099 restraints weight = 59639.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066895 restraints weight = 41529.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068110 restraints weight = 31888.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069043 restraints weight = 26205.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069626 restraints weight = 22628.169| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13009 Z= 0.121 Angle : 0.669 11.627 17579 Z= 0.326 Chirality : 0.044 0.202 2031 Planarity : 0.004 0.055 2196 Dihedral : 6.185 84.863 1772 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.67 (0.19), residues: 789 sheet: 0.42 (0.55), residues: 76 loop : -2.13 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 614 TYR 0.015 0.001 TYR A 296 PHE 0.021 0.001 PHE A1357 TRP 0.032 0.002 TRP A 116 HIS 0.012 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13003) covalent geometry : angle 0.66689 / 0.33 (17572) SS BOND : bond 0.00280 / 0.15 ( 2) SS BOND : angle 1.50374 / 0.87 ( 4) hydrogen bonds : bond 0.03144 / 2.17 ( 590) hydrogen bonds : angle 4.11069 / 2.93 ( 1704) metal coordination : bond 0.01534 / 0.77 ( 4) metal coordination : angle 4.05235 / 2.98 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.73 seconds wall clock time: 32 minutes 41.65 seconds (1961.65 seconds total)