Starting phenix.real_space_refine on Fri Sep 11 10:25:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pu7_13654/09_2026/7pu7_13654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pu7_13654/09_2026/7pu7_13654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pu7_13654/09_2026/7pu7_13654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pu7_13654/09_2026/7pu7_13654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pu7_13654/09_2026/7pu7_13654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pu7_13654/09_2026/7pu7_13654.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pu7_13654/09_2026/7pu7_13654.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pu7_13654/09_2026/7pu7_13654.cif" } resolution = 2.9 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= 0.002 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 33 5.49 5 S 37 5.16 5 C 5565 2.51 5 N 1587 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s 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: 8990 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8267 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 1 Chain: "T" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 400 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 43 Unusual residues: {' ZN': 3, '82W': 1} Classifications: {'undetermined': 4, 'water': 3} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 158 64.073 79.106 65.092 1.00 45.51 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 82W A1204 " occ=0.00 ... (35 atoms not shown) pdb=" O7 82W A1204 " occ=0.00 Time building chain proxies: 2.01, per 1000 atoms: 0.22 Number of scatterers: 8990 At special positions: 0 Unit cell: (101.322, 108.25, 112.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 37 16.00 P 33 15.00 O 1765 8.00 N 1587 7.00 C 5565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.93 Conformation dependent library (CDL) restraints added in 304.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 158 " pdb="ZN ZN A1201 " - pdb=" ND1 HIS A 107 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 14 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 16 " pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 228 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 48 " 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 56.6% alpha, 11.3% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 27 through 38 Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.546A pdb=" N SER A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.633A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 200 through 218 removed outlier: 4.148A pdb=" N VAL A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 234 through 247 removed outlier: 3.586A pdb=" N ALA A 240 " --> pdb=" O HIS A 236 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.560A pdb=" N ILE A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 4.135A pdb=" N THR A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 287 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 316 through 333 Processing helix chain 'A' and resid 340 through 355 Processing helix chain 'A' and resid 357 through 375 removed outlier: 3.965A pdb=" N PHE A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 removed outlier: 3.847A pdb=" N GLY A 387 " --> pdb=" O SER A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 400 through 405 removed outlier: 4.243A pdb=" N HIS A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 4.197A pdb=" N PHE A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.932A pdb=" N MET A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.664A pdb=" N LYS A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.592A pdb=" N ILE A 499 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 510 through 520 Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.534A pdb=" N THR A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.991A pdb=" N ILE A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 608 Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.591A pdb=" N VAL A 617 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.794A pdb=" N TYR A 625 " --> pdb=" O ASP A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 removed outlier: 3.706A pdb=" N ASP A 646 " --> pdb=" O GLY A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 665 removed outlier: 3.785A pdb=" N VAL A 659 " --> pdb=" O GLY A 655 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 663 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 664 " --> pdb=" O VAL A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.521A pdb=" N ALA A 680 " --> pdb=" O HIS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.741A pdb=" N GLU A 697 " --> pdb=" O PRO A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 726 removed outlier: 3.586A pdb=" N ILE A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 742 removed outlier: 3.540A pdb=" N ILE A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.626A pdb=" N GLU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 776 removed outlier: 3.547A pdb=" N TRP A 772 " --> pdb=" O ILE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 805 removed outlier: 3.638A pdb=" N ALA A 788 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 817 removed outlier: 3.628A pdb=" N GLY A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 816 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 835 removed outlier: 3.575A pdb=" N VAL A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 864 Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 896 through 900 Processing helix chain 'A' and resid 901 through 912 Processing helix chain 'A' and resid 920 through 940 removed outlier: 4.470A pdb=" N SER A 929 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 987 Processing helix chain 'A' and resid 998 through 1006 removed outlier: 3.884A pdb=" N GLN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1016 removed outlier: 3.635A pdb=" N ILE A1013 " --> pdb=" O ALA A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 removed outlier: 3.501A pdb=" N SER A1067 " --> pdb=" O HIS A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1072 No H-bonds generated for 'chain 'A' and resid 1070 through 1072' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 48 removed outlier: 6.695A pdb=" N VAL A 43 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY A 71 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET A 45 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A 73 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP A 47 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 75 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 14.325A pdb=" N SER A 138 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N GLU A 73 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N MET A 140 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR A 75 " --> pdb=" O MET A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 48 removed outlier: 6.695A pdb=" N VAL A 43 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY A 71 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET A 45 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A 73 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP A 47 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 75 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 70 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR A 109 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N PHE A 192 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 154 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 194 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 427 removed outlier: 6.631A pdb=" N ILE A 424 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 591 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE A 426 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 455 removed outlier: 4.143A pdb=" N ASN A 539 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 839 removed outlier: 3.542A pdb=" N ALA A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1023 through 1029 removed outlier: 6.938A pdb=" N LEU A1079 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU A1098 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASN A1081 " --> pdb=" O ASN A1096 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU A1057 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ALA A1095 " --> pdb=" O GLU A1057 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N MET A1059 " --> pdb=" O ALA A1095 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASP A1097 " --> pdb=" O MET A1059 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN A1048 " --> pdb=" O SER A1032 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N SER A1032 " --> pdb=" O GLN A1048 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1903 1.33 - 1.46: 2682 1.46 - 1.58: 4532 1.58 - 1.70: 64 1.70 - 1.82: 65 Bond restraints: 9246 Sorted by residual: bond pdb=" C4 82W A1204 " pdb=" C5 82W A1204 " ideal model delta sigma weight residual 1.510 1.356 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C1 82W A1204 " pdb=" C2 82W A1204 " ideal model delta sigma weight residual 1.532 1.381 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" C1' 82W A1204 " pdb=" C2' 82W A1204 " ideal model delta sigma weight residual 1.451 1.314 0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C13 82W A1204 " pdb=" C14 82W A1204 " ideal model delta sigma weight residual 1.510 1.374 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C6 82W A1204 " pdb=" C7 82W A1204 " ideal model delta sigma weight residual 1.500 1.367 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 9241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11501 2.24 - 4.48: 1114 4.48 - 6.71: 59 6.71 - 8.95: 5 8.95 - 11.19: 2 Bond angle restraints: 12681 Sorted by residual: angle pdb=" N LYS A 743 " pdb=" CA LYS A 743 " pdb=" C LYS A 743 " ideal model delta sigma weight residual 109.59 98.76 10.83 1.47e+00 4.63e-01 5.43e+01 angle pdb=" O4' DG T 11 " pdb=" C4' DG T 11 " pdb=" C3' DG T 11 " ideal model delta sigma weight residual 106.00 102.13 3.87 6.00e-01 2.78e+00 4.16e+01 angle pdb=" N PRO A 670 " pdb=" CA PRO A 670 " pdb=" C PRO A 670 " ideal model delta sigma weight residual 112.47 123.66 -11.19 2.06e+00 2.36e-01 2.95e+01 angle pdb=" C ALA A1009 " pdb=" N ILE A1010 " pdb=" CA ILE A1010 " ideal model delta sigma weight residual 120.24 123.52 -3.28 6.30e-01 2.52e+00 2.71e+01 angle pdb=" N ALA A1045 " pdb=" CA ALA A1045 " pdb=" C ALA A1045 " ideal model delta sigma weight residual 109.23 117.21 -7.98 1.55e+00 4.16e-01 2.65e+01 ... (remaining 12676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.65: 4999 22.65 - 45.29: 417 45.29 - 67.93: 102 67.93 - 90.58: 8 90.58 - 113.22: 1 Dihedral angle restraints: 5527 sinusoidal: 2468 harmonic: 3059 Sorted by residual: dihedral pdb=" CA SER A 20 " pdb=" C SER A 20 " pdb=" N MET A 21 " pdb=" CA MET A 21 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" C PHE A1061 " pdb=" N PHE A1061 " pdb=" CA PHE A1061 " pdb=" CB PHE A1061 " ideal model delta harmonic sigma weight residual -122.60 -133.48 10.88 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" C THR A 774 " pdb=" N THR A 774 " pdb=" CA THR A 774 " pdb=" CB THR A 774 " ideal model delta harmonic sigma weight residual -122.00 -132.04 10.04 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 898 0.092 - 0.184: 389 0.184 - 0.276: 91 0.276 - 0.367: 21 0.367 - 0.459: 3 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA PRO A 670 " pdb=" N PRO A 670 " pdb=" C PRO A 670 " pdb=" CB PRO A 670 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" C7 82W A1204 " pdb=" C12 82W A1204 " pdb=" C6 82W A1204 " pdb=" C8 82W A1204 " both_signs ideal model delta sigma weight residual False -2.93 -2.51 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA PHE A1061 " pdb=" N PHE A1061 " pdb=" C PHE A1061 " pdb=" CB PHE A1061 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 1399 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 490 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C MET A 490 " 0.036 2.00e-02 2.50e+03 pdb=" O MET A 490 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 491 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 197 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP A 197 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 197 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 198 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 563 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ARG A 563 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG A 563 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 564 " 0.010 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1909 2.80 - 3.33: 8009 3.33 - 3.85: 14131 3.85 - 4.38: 17291 4.38 - 4.90: 28396 Nonbonded interactions: 69736 Sorted by model distance: nonbonded pdb=" OD2 ASP A 23 " pdb="ZN ZN A1203 " model vdw 2.280 2.230 nonbonded pdb=" O PHE A 925 " pdb=" ND1 HIS A 928 " model vdw 2.372 3.120 nonbonded pdb=" ND2 ASN A 15 " pdb=" O GLY A 44 " model vdw 2.379 3.120 nonbonded pdb=" OD1 ASP A 842 " pdb=" N VAL A 843 " model vdw 2.481 3.120 nonbonded pdb=" O ALA A 112 " pdb=" OH TYR A 296 " model vdw 2.483 3.040 ... (remaining 69731 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.010 0.323 9252 Z= 0.582 Angle : 1.330 11.191 12681 Z= 0.920 Chirality : 0.107 0.459 1402 Planarity : 0.005 0.027 1543 Dihedral : 16.901 113.218 3573 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.28 % Allowed : 8.59 % Favored : 90.13 % Cbeta Deviations : 0.20 % 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: -1.39 (0.22), residues: 1066 helix: -0.50 (0.20), residues: 474 sheet: 0.14 (0.60), residues: 68 loop : -1.42 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 322 TYR 0.021 0.003 TYR A 392 PHE 0.021 0.003 PHE A 850 TRP 0.022 0.003 TRP A 561 HIS 0.006 0.002 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.55 ( 9246) covalent geometry : angle 1.33000 / 0.92 (12681) hydrogen bonds : bond 0.30119 / 20.36 ( 433) hydrogen bonds : angle 8.11730 / 5.76 ( 1213) metal coordination : bond 0.23335 / 14.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.285 Fit side-chains REVERT: A 196 MET cc_start: 0.8573 (ptm) cc_final: 0.8290 (ptm) REVERT: A 197 ASP cc_start: 0.8560 (t0) cc_final: 0.8286 (t0) REVERT: A 622 LYS cc_start: 0.7930 (tppt) cc_final: 0.7714 (ttpp) REVERT: A 793 MET cc_start: 0.8507 (tpt) cc_final: 0.8239 (tpt) REVERT: A 968 VAL cc_start: 0.8275 (t) cc_final: 0.7696 (t) outliers start: 11 outliers final: 2 residues processed: 128 average time/residue: 0.6971 time to fit residues: 94.4090 Evaluate side-chains 61 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 927 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 GLN A 855 GLN A 993 HIS A1063 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.111403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088785 restraints weight = 14955.661| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.13 r_work: 0.3110 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9252 Z= 0.172 Angle : 0.674 7.512 12681 Z= 0.379 Chirality : 0.047 0.222 1402 Planarity : 0.005 0.058 1543 Dihedral : 16.050 108.256 1631 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.37 % Allowed : 12.08 % Favored : 84.55 % 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: -0.09 (0.24), residues: 1066 helix: 1.15 (0.22), residues: 516 sheet: -0.34 (0.48), residues: 91 loop : -1.44 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 37 TYR 0.035 0.002 TYR A 666 PHE 0.021 0.001 PHE A 754 TRP 0.014 0.002 TRP A 561 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 ( 9246) covalent geometry : angle 0.67445 / 0.38 (12681) hydrogen bonds : bond 0.06896 / 4.61 ( 433) hydrogen bonds : angle 5.33324 / 3.81 ( 1213) metal coordination : bond 0.01009 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.351 Fit side-chains REVERT: A 85 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7327 (mtm110) REVERT: A 95 LYS cc_start: 0.7785 (tmmt) cc_final: 0.7489 (tptp) REVERT: A 416 ARG cc_start: 0.7132 (mmt-90) cc_final: 0.6821 (mtp85) REVERT: A 985 MET cc_start: 0.8129 (mmt) cc_final: 0.7920 (tpp) outliers start: 29 outliers final: 10 residues processed: 97 average time/residue: 0.5639 time to fit residues: 58.6159 Evaluate side-chains 63 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 927 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 0.0980 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088443 restraints weight = 15181.735| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.01 r_work: 0.3086 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9252 Z= 0.167 Angle : 0.620 11.038 12681 Z= 0.346 Chirality : 0.046 0.235 1402 Planarity : 0.005 0.057 1543 Dihedral : 15.847 104.054 1631 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.37 % Allowed : 14.29 % Favored : 82.35 % 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: 0.03 (0.24), residues: 1066 helix: 1.53 (0.23), residues: 502 sheet: -1.22 (0.46), residues: 100 loop : -1.41 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 119 TYR 0.025 0.002 TYR A 781 PHE 0.015 0.001 PHE A 754 TRP 0.011 0.001 TRP A 561 HIS 0.005 0.001 HIS A 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 9246) covalent geometry : angle 0.62014 / 0.35 (12681) hydrogen bonds : bond 0.05730 / 3.82 ( 433) hydrogen bonds : angle 4.94394 / 3.51 ( 1213) metal coordination : bond 0.00821 / 0.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.341 Fit side-chains REVERT: A 85 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7298 (mtm180) REVERT: A 197 ASP cc_start: 0.8030 (t0) cc_final: 0.7826 (t0) REVERT: A 416 ARG cc_start: 0.7161 (mmt-90) cc_final: 0.6834 (mtp85) REVERT: A 556 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: A 751 PHE cc_start: 0.7532 (t80) cc_final: 0.7327 (t80) REVERT: A 1084 VAL cc_start: 0.7480 (t) cc_final: 0.7092 (m) outliers start: 29 outliers final: 9 residues processed: 84 average time/residue: 0.5273 time to fit residues: 47.6730 Evaluate side-chains 67 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 927 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090181 restraints weight = 15433.745| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.03 r_work: 0.3127 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9252 Z= 0.124 Angle : 0.554 9.807 12681 Z= 0.308 Chirality : 0.043 0.235 1402 Planarity : 0.004 0.053 1543 Dihedral : 15.674 97.745 1631 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.25 % Allowed : 15.21 % Favored : 81.53 % 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: 0.29 (0.25), residues: 1066 helix: 1.72 (0.23), residues: 514 sheet: -1.20 (0.48), residues: 90 loop : -1.31 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 207 TYR 0.014 0.001 TYR A 989 PHE 0.014 0.001 PHE A 754 TRP 0.011 0.001 TRP A 561 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9246) covalent geometry : angle 0.55418 / 0.31 (12681) hydrogen bonds : bond 0.04206 / 2.80 ( 433) hydrogen bonds : angle 4.63425 / 3.29 ( 1213) metal coordination : bond 0.00224 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.332 Fit side-chains REVERT: A 271 MET cc_start: 0.8414 (mmt) cc_final: 0.8028 (mmm) REVERT: A 751 PHE cc_start: 0.7441 (t80) cc_final: 0.7175 (t80) REVERT: A 1084 VAL cc_start: 0.7318 (t) cc_final: 0.6949 (m) outliers start: 28 outliers final: 9 residues processed: 85 average time/residue: 0.5502 time to fit residues: 50.2122 Evaluate side-chains 66 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 927 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.107503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085162 restraints weight = 15297.950| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.05 r_work: 0.3027 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 9252 Z= 0.336 Angle : 0.758 9.722 12681 Z= 0.415 Chirality : 0.054 0.301 1402 Planarity : 0.007 0.067 1543 Dihedral : 15.966 94.795 1631 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.83 % Allowed : 16.96 % Favored : 79.21 % 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: -0.57 (0.24), residues: 1066 helix: 0.96 (0.22), residues: 506 sheet: -1.44 (0.48), residues: 93 loop : -1.69 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 166 TYR 0.022 0.003 TYR A 75 PHE 0.023 0.003 PHE A 850 TRP 0.012 0.002 TRP A 561 HIS 0.010 0.002 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.34 ( 9246) covalent geometry : angle 0.75813 / 0.42 (12681) hydrogen bonds : bond 0.07361 / 5.01 ( 433) hydrogen bonds : angle 5.15901 / 3.64 ( 1213) metal coordination : bond 0.01520 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 0.334 Fit side-chains REVERT: A 21 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8076 (mtm) REVERT: A 612 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8029 (mp) REVERT: A 1025 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6072 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7223 (t) cc_final: 0.6778 (m) outliers start: 33 outliers final: 14 residues processed: 81 average time/residue: 0.5012 time to fit residues: 43.9594 Evaluate side-chains 69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088636 restraints weight = 15217.651| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.07 r_work: 0.3098 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9252 Z= 0.128 Angle : 0.564 10.824 12681 Z= 0.311 Chirality : 0.043 0.234 1402 Planarity : 0.005 0.059 1543 Dihedral : 15.638 88.322 1631 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.44 % Allowed : 18.23 % Favored : 79.33 % 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: 0.05 (0.25), residues: 1066 helix: 1.54 (0.23), residues: 514 sheet: -1.41 (0.47), residues: 95 loop : -1.43 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.016 0.001 TYR A 781 PHE 0.012 0.001 PHE A 754 TRP 0.012 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 9246) covalent geometry : angle 0.56382 / 0.31 (12681) hydrogen bonds : bond 0.04418 / 2.94 ( 433) hydrogen bonds : angle 4.61188 / 3.26 ( 1213) metal coordination : bond 0.00217 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.343 Fit side-chains REVERT: A 85 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7547 (ptt180) REVERT: A 751 PHE cc_start: 0.7448 (t80) cc_final: 0.7051 (t80) REVERT: A 1084 VAL cc_start: 0.7192 (t) cc_final: 0.6786 (m) outliers start: 21 outliers final: 9 residues processed: 69 average time/residue: 0.5349 time to fit residues: 39.9032 Evaluate side-chains 62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 927 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 87 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087815 restraints weight = 15286.131| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.05 r_work: 0.3090 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9252 Z= 0.150 Angle : 0.571 11.592 12681 Z= 0.314 Chirality : 0.044 0.277 1402 Planarity : 0.005 0.056 1543 Dihedral : 15.571 81.667 1631 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.02 % Allowed : 18.00 % Favored : 78.98 % 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: 0.08 (0.25), residues: 1066 helix: 1.56 (0.23), residues: 514 sheet: -1.40 (0.47), residues: 95 loop : -1.40 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 416 TYR 0.016 0.002 TYR A 989 PHE 0.012 0.001 PHE A 754 TRP 0.010 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 9246) covalent geometry : angle 0.57102 / 0.31 (12681) hydrogen bonds : bond 0.04609 / 3.08 ( 433) hydrogen bonds : angle 4.58670 / 3.25 ( 1213) metal coordination : bond 0.00578 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.325 Fit side-chains REVERT: A 85 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7584 (ptt180) REVERT: A 196 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8408 (ptm) REVERT: A 751 PHE cc_start: 0.7444 (t80) cc_final: 0.7021 (t80) REVERT: A 1025 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6138 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7187 (t) cc_final: 0.6776 (m) REVERT: A 1087 ARG cc_start: 0.5459 (OUTLIER) cc_final: 0.5237 (mtm-85) outliers start: 26 outliers final: 11 residues processed: 72 average time/residue: 0.4963 time to fit residues: 38.7435 Evaluate side-chains 65 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1087 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.109912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087354 restraints weight = 15235.342| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.01 r_work: 0.3075 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9252 Z= 0.172 Angle : 0.597 11.662 12681 Z= 0.326 Chirality : 0.045 0.277 1402 Planarity : 0.005 0.060 1543 Dihedral : 15.577 70.555 1631 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.21 % Allowed : 18.82 % Favored : 78.98 % 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: -0.01 (0.25), residues: 1066 helix: 1.47 (0.23), residues: 514 sheet: -1.48 (0.46), residues: 98 loop : -1.42 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.018 0.002 TYR A 781 PHE 0.012 0.001 PHE A 850 TRP 0.011 0.001 TRP A 561 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9246) covalent geometry : angle 0.59699 / 0.33 (12681) hydrogen bonds : bond 0.04990 / 3.35 ( 433) hydrogen bonds : angle 4.64930 / 3.28 ( 1213) metal coordination : bond 0.00696 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.223 Fit side-chains REVERT: A 85 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7566 (ptt180) REVERT: A 196 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8415 (ptm) REVERT: A 751 PHE cc_start: 0.7443 (t80) cc_final: 0.6948 (t80) REVERT: A 1025 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6207 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7236 (t) cc_final: 0.6874 (m) REVERT: A 1087 ARG cc_start: 0.5351 (OUTLIER) cc_final: 0.5133 (mtm-85) outliers start: 19 outliers final: 12 residues processed: 68 average time/residue: 0.5587 time to fit residues: 40.8732 Evaluate side-chains 65 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1087 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 0.0570 chunk 8 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.110692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088029 restraints weight = 15161.878| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.03 r_work: 0.3091 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9252 Z= 0.145 Angle : 0.571 12.003 12681 Z= 0.311 Chirality : 0.044 0.266 1402 Planarity : 0.005 0.059 1543 Dihedral : 15.531 61.529 1631 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.97 % Allowed : 18.93 % Favored : 79.09 % 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: 0.09 (0.25), residues: 1066 helix: 1.57 (0.23), residues: 514 sheet: -1.43 (0.47), residues: 95 loop : -1.41 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.017 0.002 TYR A 989 PHE 0.011 0.001 PHE A 754 TRP 0.011 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 9246) covalent geometry : angle 0.57137 / 0.31 (12681) hydrogen bonds : bond 0.04431 / 2.95 ( 433) hydrogen bonds : angle 4.54339 / 3.21 ( 1213) metal coordination : bond 0.00507 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.330 Fit side-chains REVERT: A 85 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7570 (ptt180) REVERT: A 196 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8416 (ptm) REVERT: A 751 PHE cc_start: 0.7340 (t80) cc_final: 0.6836 (t80) REVERT: A 967 LYS cc_start: 0.7365 (tppt) cc_final: 0.7060 (tppp) REVERT: A 1025 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6218 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7179 (t) cc_final: 0.6837 (m) REVERT: A 1087 ARG cc_start: 0.5351 (OUTLIER) cc_final: 0.5121 (mtm-85) outliers start: 17 outliers final: 11 residues processed: 69 average time/residue: 0.5893 time to fit residues: 43.6459 Evaluate side-chains 67 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1087 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 12 optimal weight: 0.0370 chunk 48 optimal weight: 0.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.109789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087233 restraints weight = 15215.954| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.04 r_work: 0.3077 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9252 Z= 0.177 Angle : 0.601 11.956 12681 Z= 0.326 Chirality : 0.045 0.260 1402 Planarity : 0.005 0.058 1543 Dihedral : 15.580 59.763 1631 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.86 % Allowed : 19.16 % Favored : 78.98 % 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: -0.04 (0.25), residues: 1066 helix: 1.46 (0.23), residues: 514 sheet: -1.47 (0.47), residues: 98 loop : -1.47 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.018 0.002 TYR A 989 PHE 0.013 0.001 PHE A 850 TRP 0.010 0.001 TRP A 561 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 9246) covalent geometry : angle 0.60133 / 0.33 (12681) hydrogen bonds : bond 0.04981 / 3.35 ( 433) hydrogen bonds : angle 4.62143 / 3.26 ( 1213) metal coordination : bond 0.00716 / 0.48 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.347 Fit side-chains REVERT: A 85 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7579 (ptt180) REVERT: A 196 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8398 (ptm) REVERT: A 751 PHE cc_start: 0.7300 (t80) cc_final: 0.6790 (t80) REVERT: A 967 LYS cc_start: 0.7388 (tppt) cc_final: 0.7061 (tppp) REVERT: A 1025 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6189 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7124 (t) cc_final: 0.6762 (m) outliers start: 16 outliers final: 11 residues processed: 67 average time/residue: 0.5864 time to fit residues: 42.2146 Evaluate side-chains 66 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088791 restraints weight = 14972.023| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.99 r_work: 0.3112 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9252 Z= 0.129 Angle : 0.571 14.476 12681 Z= 0.309 Chirality : 0.043 0.259 1402 Planarity : 0.004 0.058 1543 Dihedral : 15.494 59.865 1631 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.86 % Allowed : 19.40 % Favored : 78.75 % 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: 0.18 (0.25), residues: 1066 helix: 1.66 (0.23), residues: 514 sheet: -1.32 (0.48), residues: 95 loop : -1.39 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1087 TYR 0.018 0.001 TYR A 989 PHE 0.012 0.001 PHE A 754 TRP 0.011 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9246) covalent geometry : angle 0.57089 / 0.31 (12681) hydrogen bonds : bond 0.04072 / 2.70 ( 433) hydrogen bonds : angle 4.45679 / 3.15 ( 1213) metal coordination : bond 0.00366 / 0.24 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.59 seconds wall clock time: 44 minutes 54.19 seconds (2694.19 seconds total)