Starting phenix.real_space_refine on Tue Mar 3 22:22:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pu7_13654/03_2026/7pu7_13654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pu7_13654/03_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_13654/03_2026/7pu7_13654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pu7_13654/03_2026/7pu7_13654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pu7_13654/03_2026/7pu7_13654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pu7_13654/03_2026/7pu7_13654.map" } 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-dev-5986/lib/python3.9/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: 2.31, per 1000 atoms: 0.26 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: 0.95 Conformation dependent library (CDL) restraints added in 488.5 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: 1.36 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: 2.02 Time building geometry restraints manager: 1.23 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: 11489 2.24 - 4.48: 1127 4.48 - 6.71: 58 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=" 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 angle pdb=" C MET A 671 " pdb=" N GLY A 672 " pdb=" CA GLY A 672 " ideal model delta sigma weight residual 120.00 125.21 -5.21 1.10e+00 8.26e-01 2.24e+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: 900 0.092 - 0.184: 389 0.184 - 0.276: 89 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: 1.160 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: 0.030 Set scattering table: 0.020 Process input model: 13.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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= 0.561 Angle : 1.335 11.191 12681 Z= 0.916 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 covalent geometry : bond 0.00830 ( 9246) covalent geometry : angle 1.33517 (12681) hydrogen bonds : bond 0.30119 ( 433) hydrogen bonds : angle 8.11730 ( 1213) metal coordination : bond 0.23335 ( 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 : 0.312 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: 0.7253 time to fit residues: 97.9335 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 : 0.324 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 687 GLN A 855 GLN A 993 HIS A1063 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089015 restraints weight = 15019.331| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.22 r_work: 0.3118 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9252 Z= 0.161 Angle : 0.639 7.194 12681 Z= 0.351 Chirality : 0.045 0.224 1402 Planarity : 0.005 0.048 1543 Dihedral : 15.834 107.980 1631 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.02 % Allowed : 12.66 % Favored : 84.32 % 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: 0.02 (0.24), residues: 1066 helix: 1.25 (0.23), residues: 516 sheet: -0.23 (0.49), residues: 91 loop : -1.39 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.033 0.002 TYR A 666 PHE 0.016 0.001 PHE A 754 TRP 0.014 0.001 TRP A1044 HIS 0.004 0.001 HIS A1063 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9246) covalent geometry : angle 0.63908 (12681) hydrogen bonds : bond 0.05584 ( 433) hydrogen bonds : angle 5.15692 ( 1213) metal coordination : bond 0.00775 ( 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 104 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.334 Fit side-chains REVERT: A 85 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7364 (mtm110) REVERT: A 95 LYS cc_start: 0.7743 (tmmt) cc_final: 0.7467 (tptp) REVERT: A 524 ARG cc_start: 0.7622 (ttp-110) cc_final: 0.7260 (ttp-110) REVERT: A 1084 VAL cc_start: 0.7401 (t) cc_final: 0.7000 (m) outliers start: 26 outliers final: 9 residues processed: 95 average time/residue: 0.6150 time to fit residues: 62.3990 Evaluate side-chains 62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087026 restraints weight = 15198.415| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.08 r_work: 0.3067 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9252 Z= 0.205 Angle : 0.644 10.751 12681 Z= 0.351 Chirality : 0.046 0.234 1402 Planarity : 0.005 0.059 1543 Dihedral : 15.678 104.533 1631 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.83 % Allowed : 14.05 % Favored : 82.11 % 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: -0.07 (0.25), residues: 1066 helix: 1.33 (0.23), residues: 512 sheet: -1.21 (0.47), residues: 93 loop : -1.40 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 37 TYR 0.016 0.002 TYR A 75 PHE 0.014 0.002 PHE A 754 TRP 0.013 0.002 TRP A 561 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 9246) covalent geometry : angle 0.64423 (12681) hydrogen bonds : bond 0.05911 ( 433) hydrogen bonds : angle 4.96291 ( 1213) metal coordination : bond 0.00827 ( 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 94 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.322 Fit side-chains REVERT: A 21 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.7929 (mtm) REVERT: A 85 ARG cc_start: 0.7788 (mtm110) cc_final: 0.7292 (mtm180) REVERT: A 556 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8239 (mm-30) REVERT: A 1084 VAL cc_start: 0.7351 (t) cc_final: 0.6954 (m) outliers start: 33 outliers final: 14 residues processed: 82 average time/residue: 0.5692 time to fit residues: 50.0508 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 : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 99 VAL 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 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 670 PRO 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 102 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089037 restraints weight = 15470.725| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.11 r_work: 0.3108 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9252 Z= 0.135 Angle : 0.557 9.822 12681 Z= 0.303 Chirality : 0.043 0.261 1402 Planarity : 0.004 0.058 1543 Dihedral : 15.340 99.352 1631 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.90 % Allowed : 15.80 % Favored : 81.30 % 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: 0.20 (0.25), residues: 1066 helix: 1.63 (0.23), residues: 514 sheet: -1.25 (0.47), residues: 95 loop : -1.33 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.016 0.002 TYR A 781 PHE 0.013 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 covalent geometry : bond 0.00300 ( 9246) covalent geometry : angle 0.55669 (12681) hydrogen bonds : bond 0.04217 ( 433) hydrogen bonds : angle 4.63495 ( 1213) metal coordination : bond 0.00386 ( 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 87 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.356 Fit side-chains REVERT: A 750 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7117 (mp0) REVERT: A 1084 VAL cc_start: 0.7296 (t) cc_final: 0.6910 (m) outliers start: 25 outliers final: 9 residues processed: 78 average time/residue: 0.5591 time to fit residues: 47.0592 Evaluate side-chains 64 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 735 LEU Chi-restraints excluded: chain A residue 896 ASP 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: 3.9990 chunk 31 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 0.0270 chunk 108 optimal weight: 4.9990 overall best weight: 2.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.109927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087327 restraints weight = 15352.561| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.03 r_work: 0.3078 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9252 Z= 0.183 Angle : 0.593 10.617 12681 Z= 0.321 Chirality : 0.045 0.272 1402 Planarity : 0.005 0.057 1543 Dihedral : 15.373 93.750 1631 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.37 % Allowed : 16.38 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1066 helix: 1.55 (0.23), residues: 514 sheet: -1.39 (0.46), residues: 98 loop : -1.34 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.013 0.002 TYR A 989 PHE 0.012 0.002 PHE A 754 TRP 0.012 0.001 TRP A 561 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9246) covalent geometry : angle 0.59303 (12681) hydrogen bonds : bond 0.05047 ( 433) hydrogen bonds : angle 4.67555 ( 1213) metal coordination : bond 0.00691 ( 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: 29 poor density : 58 time to evaluate : 0.315 Fit side-chains REVERT: A 21 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.7857 (mtm) REVERT: A 85 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7570 (ptt180) REVERT: A 967 LYS cc_start: 0.7387 (tppt) cc_final: 0.7018 (tppp) REVERT: A 1084 VAL cc_start: 0.7193 (t) cc_final: 0.6778 (m) outliers start: 29 outliers final: 15 residues processed: 77 average time/residue: 0.5091 time to fit residues: 42.5395 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 : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET 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 350 ASP 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 586 MET Chi-restraints excluded: chain A residue 627 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 965 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.110968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088438 restraints weight = 15379.095| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.04 r_work: 0.3097 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9252 Z= 0.143 Angle : 0.550 11.072 12681 Z= 0.297 Chirality : 0.043 0.267 1402 Planarity : 0.004 0.057 1543 Dihedral : 15.208 86.129 1631 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.25 % Allowed : 16.49 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1066 helix: 1.70 (0.23), residues: 514 sheet: -1.41 (0.46), residues: 95 loop : -1.31 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.015 0.002 TYR A 989 PHE 0.013 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 covalent geometry : bond 0.00326 ( 9246) covalent geometry : angle 0.55049 (12681) hydrogen bonds : bond 0.04205 ( 433) hydrogen bonds : angle 4.50815 ( 1213) metal coordination : bond 0.00491 ( 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 88 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.335 Fit side-chains REVERT: A 40 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8358 (mtt) REVERT: A 85 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7559 (ptt180) REVERT: A 271 MET cc_start: 0.8349 (mmt) cc_final: 0.8020 (mmm) REVERT: A 490 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.4889 (mtt) REVERT: A 967 LYS cc_start: 0.7371 (tppt) cc_final: 0.7087 (tppp) REVERT: A 1025 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6230 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7238 (t) cc_final: 0.6869 (m) outliers start: 28 outliers final: 13 residues processed: 78 average time/residue: 0.5794 time to fit residues: 48.5908 Evaluate side-chains 72 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 490 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 735 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 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: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086538 restraints weight = 15376.787| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.03 r_work: 0.3063 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9252 Z= 0.220 Angle : 0.626 11.269 12681 Z= 0.338 Chirality : 0.047 0.278 1402 Planarity : 0.005 0.057 1543 Dihedral : 15.353 77.580 1631 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.37 % Allowed : 16.96 % Favored : 79.67 % 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: -0.12 (0.25), residues: 1066 helix: 1.38 (0.23), residues: 513 sheet: -1.53 (0.45), residues: 98 loop : -1.46 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.017 0.002 TYR A 989 PHE 0.015 0.002 PHE A 850 TRP 0.011 0.001 TRP A 561 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 9246) covalent geometry : angle 0.62562 (12681) hydrogen bonds : bond 0.05444 ( 433) hydrogen bonds : angle 4.71943 ( 1213) metal coordination : bond 0.00863 ( 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 86 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.325 Fit side-chains REVERT: A 21 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.7915 (mtm) REVERT: A 85 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7548 (ptt180) REVERT: A 490 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.4739 (mtt) REVERT: A 586 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8262 (mtt) REVERT: A 967 LYS cc_start: 0.7390 (tppt) cc_final: 0.7096 (tppp) REVERT: A 1025 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6223 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7060 (t) cc_final: 0.6678 (m) outliers start: 29 outliers final: 13 residues processed: 77 average time/residue: 0.5255 time to fit residues: 43.8394 Evaluate side-chains 71 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 227 CYS 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 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 627 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.110551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088126 restraints weight = 15240.591| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.01 r_work: 0.3089 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9252 Z= 0.149 Angle : 0.564 11.796 12681 Z= 0.304 Chirality : 0.043 0.259 1402 Planarity : 0.005 0.059 1543 Dihedral : 15.193 67.692 1631 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.21 % Allowed : 18.23 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1066 helix: 1.62 (0.23), residues: 514 sheet: -1.51 (0.46), residues: 95 loop : -1.39 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.016 0.002 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 covalent geometry : bond 0.00339 ( 9246) covalent geometry : angle 0.56416 (12681) hydrogen bonds : bond 0.04315 ( 433) hydrogen bonds : angle 4.51004 ( 1213) metal coordination : bond 0.00526 ( 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 76 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.342 Fit side-chains REVERT: A 85 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7546 (ptt180) REVERT: A 196 MET cc_start: 0.8553 (ptm) cc_final: 0.8303 (ptm) REVERT: A 271 MET cc_start: 0.8379 (mmt) cc_final: 0.7984 (mmm) REVERT: A 490 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.4694 (mtt) REVERT: A 967 LYS cc_start: 0.7393 (tppt) cc_final: 0.7118 (tppp) REVERT: A 1025 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6247 (tmm-80) outliers start: 19 outliers final: 12 residues processed: 70 average time/residue: 0.5169 time to fit residues: 39.0491 Evaluate side-chains 68 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 350 ASP 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 490 MET Chi-restraints excluded: chain A residue 586 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087827 restraints weight = 15195.078| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.05 r_work: 0.3088 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9252 Z= 0.156 Angle : 0.577 11.995 12681 Z= 0.309 Chirality : 0.044 0.248 1402 Planarity : 0.005 0.058 1543 Dihedral : 15.174 59.918 1631 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.79 % Allowed : 18.00 % 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: 0.11 (0.25), residues: 1066 helix: 1.58 (0.23), residues: 514 sheet: -1.47 (0.46), residues: 95 loop : -1.37 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.018 0.002 TYR A 989 PHE 0.013 0.001 PHE A 754 TRP 0.011 0.001 TRP A 561 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9246) covalent geometry : angle 0.57703 (12681) hydrogen bonds : bond 0.04432 ( 433) hydrogen bonds : angle 4.48596 ( 1213) metal coordination : bond 0.00543 ( 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 79 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.313 Fit side-chains REVERT: A 85 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7547 (ptt180) REVERT: A 196 MET cc_start: 0.8642 (ptm) cc_final: 0.8361 (ptm) REVERT: A 490 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.4750 (mtt) REVERT: A 612 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 967 LYS cc_start: 0.7376 (tppt) cc_final: 0.7120 (tppp) REVERT: A 1025 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6244 (tmm-80) REVERT: A 1087 ARG cc_start: 0.5383 (OUTLIER) cc_final: 0.5176 (mtm-85) outliers start: 24 outliers final: 13 residues processed: 74 average time/residue: 0.5627 time to fit residues: 44.8351 Evaluate side-chains 70 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 227 CYS 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 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 612 LEU 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: 0.8980 chunk 105 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 104 optimal weight: 0.0060 chunk 74 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 12 optimal weight: 0.0270 chunk 48 optimal weight: 2.9990 overall best weight: 0.7456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090038 restraints weight = 15244.246| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.03 r_work: 0.3131 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3608 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= 0.117 Angle : 0.546 13.230 12681 Z= 0.290 Chirality : 0.042 0.237 1402 Planarity : 0.004 0.055 1543 Dihedral : 14.980 59.474 1631 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.09 % Allowed : 19.05 % Favored : 78.86 % 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: 1.75 (0.23), residues: 516 sheet: -1.53 (0.44), residues: 105 loop : -1.26 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.019 0.001 TYR A 989 PHE 0.013 0.001 PHE A 754 TRP 0.009 0.001 TRP A 561 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9246) covalent geometry : angle 0.54624 (12681) hydrogen bonds : bond 0.03444 ( 433) hydrogen bonds : angle 4.31408 ( 1213) metal coordination : bond 0.00272 ( 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 76 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.343 Fit side-chains REVERT: A 85 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7561 (ptt180) REVERT: A 196 MET cc_start: 0.8602 (ptm) cc_final: 0.8325 (ptm) REVERT: A 490 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.4615 (mtt) REVERT: A 1025 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6218 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7140 (t) cc_final: 0.6796 (m) outliers start: 18 outliers final: 11 residues processed: 71 average time/residue: 0.6110 time to fit residues: 46.5548 Evaluate side-chains 65 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 227 CYS 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 490 MET 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: 2.9990 chunk 87 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.111201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088880 restraints weight = 15021.157| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.98 r_work: 0.3101 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3557 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= 0.149 Angle : 0.598 18.655 12681 Z= 0.312 Chirality : 0.043 0.238 1402 Planarity : 0.004 0.055 1543 Dihedral : 15.040 59.655 1631 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.97 % Allowed : 19.16 % Favored : 78.86 % 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: 0.21 (0.25), residues: 1066 helix: 1.66 (0.23), residues: 516 sheet: -1.53 (0.44), residues: 105 loop : -1.27 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.018 0.001 TYR A 989 PHE 0.013 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 covalent geometry : bond 0.00342 ( 9246) covalent geometry : angle 0.59764 (12681) hydrogen bonds : bond 0.04099 ( 433) hydrogen bonds : angle 4.39906 ( 1213) metal coordination : bond 0.00483 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.27 seconds wall clock time: 47 minutes 46.11 seconds (2866.11 seconds total)