Starting phenix.real_space_refine on Thu Mar 13 15:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pu7_13654/03_2025/7pu7_13654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pu7_13654/03_2025/7pu7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pu7_13654/03_2025/7pu7_13654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pu7_13654/03_2025/7pu7_13654.map" model { file = "/net/cci-nas-00/data/ceres_data/7pu7_13654/03_2025/7pu7_13654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pu7_13654/03_2025/7pu7_13654.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.03, per 1000 atoms: 0.67 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.15 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: 3.82 Time building geometry restraints manager: 2.88 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- 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 : 0.008 0.154 9246 Z= 0.507 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.003 TRP A 561 HIS 0.006 0.002 HIS A 48 PHE 0.021 0.003 PHE A 850 TYR 0.021 0.003 TYR A 392 ARG 0.006 0.001 ARG A 322 *********************** 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 : 0.914 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: 0.8283 (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: 1.4001 time to fit residues: 189.8438 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 : 0.891 ------------------------------------------------------------------------------- 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 92 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.0000 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 273 GLN A 687 GLN A 855 GLN A 993 HIS A1063 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089680 restraints weight = 14872.293| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.13 r_work: 0.3120 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9246 Z= 0.215 Angle : 0.640 7.261 12681 Z= 0.351 Chirality : 0.045 0.221 1402 Planarity : 0.005 0.047 1543 Dihedral : 15.850 107.978 1631 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.14 % Allowed : 12.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1066 helix: 1.32 (0.23), residues: 516 sheet: -0.23 (0.49), residues: 91 loop : -1.38 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1044 HIS 0.005 0.001 HIS A1063 PHE 0.017 0.001 PHE A 754 TYR 0.035 0.002 TYR A 666 ARG 0.006 0.000 ARG A 37 *********************** 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 105 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7350 (mtm110) REVERT: A 95 LYS cc_start: 0.7742 (tmmt) cc_final: 0.7468 (tptp) REVERT: A 524 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7249 (ttp-110) REVERT: A 1084 VAL cc_start: 0.7384 (t) cc_final: 0.6983 (m) outliers start: 27 outliers final: 10 residues processed: 96 average time/residue: 1.2128 time to fit residues: 125.1922 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 : 0.987 ------------------------------------------------------------------------------- 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 915 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 104 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 chunk 86 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.113368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091330 restraints weight = 15230.282| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.02 r_work: 0.3149 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9246 Z= 0.176 Angle : 0.560 12.496 12681 Z= 0.301 Chirality : 0.042 0.226 1402 Planarity : 0.004 0.060 1543 Dihedral : 15.363 99.502 1631 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.37 % Allowed : 13.82 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1066 helix: 1.83 (0.23), residues: 510 sheet: -0.99 (0.47), residues: 100 loop : -1.16 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 561 HIS 0.003 0.001 HIS A 504 PHE 0.014 0.001 PHE A 754 TYR 0.016 0.001 TYR A 666 ARG 0.005 0.000 ARG A 37 *********************** 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 100 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.916 Fit side-chains REVERT: A 524 ARG cc_start: 0.7529 (ttp-110) cc_final: 0.7107 (ttp-110) REVERT: A 750 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7147 (mp0) REVERT: A 1036 ARG cc_start: 0.5893 (mtt180) cc_final: 0.4905 (mmm-85) REVERT: A 1084 VAL cc_start: 0.7350 (t) cc_final: 0.7007 (m) outliers start: 29 outliers final: 8 residues processed: 89 average time/residue: 1.2348 time to fit residues: 117.7728 Evaluate side-chains 69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 627 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.113685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091251 restraints weight = 15104.539| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.96 r_work: 0.3158 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9246 Z= 0.165 Angle : 0.524 9.871 12681 Z= 0.284 Chirality : 0.041 0.262 1402 Planarity : 0.004 0.056 1543 Dihedral : 15.166 91.428 1630 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.79 % Allowed : 14.63 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1066 helix: 1.98 (0.23), residues: 508 sheet: -1.02 (0.48), residues: 95 loop : -1.15 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 PHE 0.011 0.001 PHE A 778 TYR 0.018 0.001 TYR A 781 ARG 0.004 0.000 ARG A 37 *********************** 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 94 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.928 Fit side-chains REVERT: A 524 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.7123 (ttp-110) REVERT: A 756 ASP cc_start: 0.7633 (t0) cc_final: 0.7401 (t0) REVERT: A 1036 ARG cc_start: 0.5781 (mtt180) cc_final: 0.4970 (mmm-85) REVERT: A 1084 VAL cc_start: 0.7354 (t) cc_final: 0.7019 (m) outliers start: 24 outliers final: 10 residues processed: 88 average time/residue: 1.2365 time to fit residues: 116.9429 Evaluate side-chains 69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 627 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.110690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088207 restraints weight = 15134.696| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.93 r_work: 0.3098 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9246 Z= 0.257 Angle : 0.578 10.675 12681 Z= 0.313 Chirality : 0.045 0.274 1402 Planarity : 0.005 0.055 1543 Dihedral : 15.236 82.936 1630 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.60 % Allowed : 14.98 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1066 helix: 1.79 (0.23), residues: 506 sheet: -1.34 (0.46), residues: 95 loop : -1.25 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 PHE 0.014 0.001 PHE A 778 TYR 0.016 0.002 TYR A 989 ARG 0.004 0.000 ARG A 166 *********************** 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 88 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 1.002 Fit side-chains REVERT: A 490 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.5304 (mtt) REVERT: A 756 ASP cc_start: 0.7673 (t0) cc_final: 0.7453 (t0) REVERT: A 1084 VAL cc_start: 0.7361 (t) cc_final: 0.6995 (m) outliers start: 31 outliers final: 12 residues processed: 78 average time/residue: 1.0271 time to fit residues: 87.6393 Evaluate side-chains 69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 99 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.108302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085841 restraints weight = 15175.917| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.95 r_work: 0.3046 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9246 Z= 0.419 Angle : 0.675 10.477 12681 Z= 0.365 Chirality : 0.049 0.293 1402 Planarity : 0.006 0.058 1543 Dihedral : 15.480 71.257 1630 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.60 % Allowed : 15.91 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1066 helix: 1.18 (0.22), residues: 514 sheet: -1.51 (0.47), residues: 93 loop : -1.43 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 561 HIS 0.008 0.002 HIS A 323 PHE 0.019 0.002 PHE A 778 TYR 0.019 0.003 TYR A 625 ARG 0.005 0.001 ARG A 166 *********************** 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 92 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.919 Fit side-chains REVERT: A 21 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8099 (mtm) REVERT: A 40 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: A 85 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7594 (ptt180) REVERT: A 751 PHE cc_start: 0.7523 (t80) cc_final: 0.7313 (t80) REVERT: A 756 ASP cc_start: 0.7756 (t0) cc_final: 0.7548 (t0) REVERT: A 1084 VAL cc_start: 0.7202 (t) cc_final: 0.6793 (m) outliers start: 31 outliers final: 16 residues processed: 81 average time/residue: 1.1605 time to fit residues: 103.0354 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 : 1.225 ------------------------------------------------------------------------------- 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 425 ASP 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 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 Chi-restraints excluded: chain A residue 1013 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.112261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089831 restraints weight = 15234.049| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.97 r_work: 0.3128 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9246 Z= 0.164 Angle : 0.530 11.472 12681 Z= 0.285 Chirality : 0.041 0.246 1402 Planarity : 0.004 0.058 1543 Dihedral : 15.109 62.554 1630 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.32 % Allowed : 17.89 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1066 helix: 1.70 (0.23), residues: 516 sheet: -1.43 (0.48), residues: 90 loop : -1.29 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.003 0.001 HIS A 323 PHE 0.012 0.001 PHE A 754 TYR 0.015 0.001 TYR A 989 ARG 0.003 0.000 ARG A 37 *********************** 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 85 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 1.040 Fit side-chains REVERT: A 85 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7899 (mtm110) REVERT: A 490 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.5032 (mtt) REVERT: A 756 ASP cc_start: 0.7747 (t0) cc_final: 0.7537 (t0) REVERT: A 1025 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6112 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7163 (t) cc_final: 0.6819 (m) outliers start: 20 outliers final: 10 residues processed: 80 average time/residue: 1.2777 time to fit residues: 110.1338 Evaluate side-chains 68 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL 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 627 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 758 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.108752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086284 restraints weight = 15391.250| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.98 r_work: 0.3053 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9246 Z= 0.401 Angle : 0.659 11.533 12681 Z= 0.353 Chirality : 0.048 0.268 1402 Planarity : 0.005 0.056 1543 Dihedral : 15.388 59.949 1630 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.90 % Allowed : 17.65 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1066 helix: 1.31 (0.23), residues: 514 sheet: -1.50 (0.48), residues: 93 loop : -1.48 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 561 HIS 0.007 0.002 HIS A 323 PHE 0.018 0.002 PHE A 778 TYR 0.017 0.002 TYR A 625 ARG 0.004 0.001 ARG A 272 *********************** 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 82 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 1.029 Fit side-chains REVERT: A 490 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.4831 (mtt) REVERT: A 751 PHE cc_start: 0.7450 (t80) cc_final: 0.7217 (t80) REVERT: A 1025 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6177 (tmm-80) outliers start: 25 outliers final: 12 residues processed: 74 average time/residue: 1.1781 time to fit residues: 94.2337 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 : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.109487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086089 restraints weight = 15280.239| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.24 r_work: 0.3068 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9246 Z= 0.227 Angle : 0.577 11.924 12681 Z= 0.309 Chirality : 0.043 0.251 1402 Planarity : 0.004 0.058 1543 Dihedral : 15.203 59.660 1630 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.44 % Allowed : 19.16 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1066 helix: 1.54 (0.23), residues: 514 sheet: -1.44 (0.48), residues: 90 loop : -1.42 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 PHE 0.012 0.001 PHE A 778 TYR 0.018 0.002 TYR A 989 ARG 0.003 0.000 ARG A 37 *********************** 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 78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 1.037 Fit side-chains REVERT: A 85 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7623 (ptt180) REVERT: A 196 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8299 (ptm) REVERT: A 490 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.4754 (mtt) REVERT: A 773 ASP cc_start: 0.8274 (t0) cc_final: 0.8009 (p0) REVERT: A 774 THR cc_start: 0.8750 (t) cc_final: 0.8317 (m) REVERT: A 1025 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6078 (tmm-80) outliers start: 21 outliers final: 14 residues processed: 73 average time/residue: 1.2211 time to fit residues: 96.0564 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 : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 140 MET 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 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 758 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 97 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.109572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086047 restraints weight = 15249.812| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.27 r_work: 0.3073 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9246 Z= 0.229 Angle : 0.577 11.986 12681 Z= 0.308 Chirality : 0.043 0.248 1402 Planarity : 0.004 0.055 1543 Dihedral : 15.157 59.957 1630 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.21 % Allowed : 19.40 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1066 helix: 1.56 (0.23), residues: 514 sheet: -1.38 (0.49), residues: 90 loop : -1.40 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.001 PHE A 754 TYR 0.018 0.002 TYR A 989 ARG 0.002 0.000 ARG A 332 ********************** 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 74 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.938 Fit side-chains REVERT: A 85 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7700 (ptt180) REVERT: A 196 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8324 (ptm) REVERT: A 490 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.4805 (mtt) REVERT: A 773 ASP cc_start: 0.8275 (t0) cc_final: 0.8037 (p0) REVERT: A 774 THR cc_start: 0.8742 (t) cc_final: 0.8351 (m) REVERT: A 1025 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6110 (tmm-80) outliers start: 19 outliers final: 12 residues processed: 68 average time/residue: 1.1863 time to fit residues: 87.1493 Evaluate side-chains 68 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 735 LEU Chi-restraints excluded: chain A residue 758 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 71 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.110651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087860 restraints weight = 15211.328| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.03 r_work: 0.3089 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9246 Z= 0.244 Angle : 0.583 11.944 12681 Z= 0.311 Chirality : 0.044 0.249 1402 Planarity : 0.005 0.056 1543 Dihedral : 15.143 59.854 1630 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.09 % Allowed : 19.86 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1066 helix: 1.52 (0.23), residues: 514 sheet: -1.41 (0.49), residues: 90 loop : -1.41 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 PHE 0.013 0.001 PHE A 778 TYR 0.018 0.002 TYR A 989 ARG 0.002 0.000 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5428.39 seconds wall clock time: 95 minutes 27.53 seconds (5727.53 seconds total)