Starting phenix.real_space_refine on Thu Feb 13 12:52:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pu7_13654/02_2025/7pu7_13654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pu7_13654/02_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_13654/02_2025/7pu7_13654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pu7_13654/02_2025/7pu7_13654.map" model { file = "/net/cci-nas-00/data/ceres_data/7pu7_13654/02_2025/7pu7_13654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pu7_13654/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.54, per 1000 atoms: 0.62 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: 2.67 Conformation dependent library (CDL) restraints added in 1.1 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: 3.25 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: 4.44 Time building geometry restraints manager: 3.04 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: 0.900 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.360 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:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- 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 : 0.983 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: 1.4537 time to fit residues: 197.1676 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 : 0.964 ------------------------------------------------------------------------------- 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 = 14872.313| |-----------------------------------------------------------------------------| 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 : 0.895 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7709 (mtm110) cc_final: 0.7349 (mtm110) REVERT: A 95 LYS cc_start: 0.7741 (tmmt) cc_final: 0.7466 (tptp) REVERT: A 524 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7248 (ttp-110) REVERT: A 1084 VAL cc_start: 0.7383 (t) cc_final: 0.6982 (m) outliers start: 27 outliers final: 10 residues processed: 96 average time/residue: 1.1869 time to fit residues: 122.5107 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 : 0.973 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.112783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090624 restraints weight = 15241.385| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.07 r_work: 0.3130 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9246 Z= 0.184 Angle : 0.565 12.131 12681 Z= 0.305 Chirality : 0.042 0.219 1402 Planarity : 0.004 0.059 1543 Dihedral : 15.370 99.667 1631 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.37 % Allowed : 14.05 % 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: 0.43 (0.25), residues: 1066 helix: 1.79 (0.23), residues: 512 sheet: -1.05 (0.46), residues: 100 loop : -1.18 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.003 0.001 HIS A 928 PHE 0.014 0.001 PHE A 754 TYR 0.014 0.001 TYR A 989 ARG 0.004 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 99 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.960 Fit side-chains REVERT: A 85 ARG cc_start: 0.7798 (mtm110) cc_final: 0.7298 (mtm180) REVERT: A 524 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.7136 (ttp-110) REVERT: A 750 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7116 (mp0) REVERT: A 1084 VAL cc_start: 0.7332 (t) cc_final: 0.6974 (m) outliers start: 29 outliers final: 7 residues processed: 88 average time/residue: 1.3659 time to fit residues: 129.1290 Evaluate side-chains 69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 52 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 56 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 33 optimal weight: 0.0270 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.113212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090907 restraints weight = 15113.739| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.92 r_work: 0.3152 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3014 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= 0.167 Angle : 0.525 10.128 12681 Z= 0.284 Chirality : 0.042 0.265 1402 Planarity : 0.004 0.056 1543 Dihedral : 15.170 91.221 1630 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.25 % Allowed : 14.40 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.25), residues: 1066 helix: 1.97 (0.23), residues: 508 sheet: -1.05 (0.47), residues: 95 loop : -1.18 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 561 HIS 0.002 0.001 HIS A 323 PHE 0.011 0.001 PHE A 754 TYR 0.017 0.001 TYR A 781 ARG 0.003 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 98 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 1.280 Fit side-chains REVERT: A 524 ARG cc_start: 0.7533 (ttp-110) cc_final: 0.7098 (ttp-110) REVERT: A 622 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7292 (ttpt) REVERT: A 756 ASP cc_start: 0.7680 (t0) cc_final: 0.7470 (t0) REVERT: A 1036 ARG cc_start: 0.5822 (mtt180) cc_final: 0.5024 (mmm-85) REVERT: A 1084 VAL cc_start: 0.7366 (t) cc_final: 0.7034 (m) outliers start: 28 outliers final: 12 residues processed: 91 average time/residue: 1.2229 time to fit residues: 120.0050 Evaluate side-chains 74 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 622 LYS 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: 0.7980 chunk 70 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.108322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085631 restraints weight = 15236.472| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.01 r_work: 0.3046 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 9246 Z= 0.463 Angle : 0.698 10.268 12681 Z= 0.379 Chirality : 0.051 0.277 1402 Planarity : 0.006 0.054 1543 Dihedral : 15.566 87.280 1630 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.83 % Allowed : 15.45 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.24), residues: 1066 helix: 1.18 (0.22), residues: 513 sheet: -1.52 (0.46), residues: 98 loop : -1.41 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 561 HIS 0.009 0.002 HIS A 323 PHE 0.018 0.002 PHE A 850 TYR 0.019 0.003 TYR A 625 ARG 0.005 0.001 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 95 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.935 Fit side-chains REVERT: A 21 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8117 (mtm) REVERT: A 85 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7575 (ptt180) REVERT: A 586 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8380 (mtt) REVERT: A 756 ASP cc_start: 0.7617 (t0) cc_final: 0.7411 (t0) REVERT: A 1084 VAL cc_start: 0.7240 (t) cc_final: 0.6826 (m) outliers start: 33 outliers final: 15 residues processed: 85 average time/residue: 1.0480 time to fit residues: 97.0218 Evaluate side-chains 77 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 206 VAL 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 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: 10.0000 chunk 42 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.112462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089901 restraints weight = 15105.973| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.99 r_work: 0.3131 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3328 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= 0.171 Angle : 0.533 10.934 12681 Z= 0.288 Chirality : 0.042 0.242 1402 Planarity : 0.004 0.056 1543 Dihedral : 15.114 77.385 1630 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.44 % Allowed : 17.54 % Favored : 80.02 % 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: 0.31 (0.25), residues: 1066 helix: 1.73 (0.23), residues: 516 sheet: -1.40 (0.48), residues: 90 loop : -1.25 (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 0.014 0.001 TYR A 989 ARG 0.004 0.000 ARG A 37 *********************** 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 85 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.947 Fit side-chains REVERT: A 85 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7897 (mtm110) REVERT: A 490 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.5109 (mtt) REVERT: A 756 ASP cc_start: 0.7752 (t0) cc_final: 0.7539 (t0) REVERT: A 1025 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6065 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7244 (t) cc_final: 0.6903 (m) outliers start: 21 outliers final: 9 residues processed: 78 average time/residue: 1.2034 time to fit residues: 101.0659 Evaluate side-chains 67 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.109255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086573 restraints weight = 15246.381| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.04 r_work: 0.3061 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9246 Z= 0.347 Angle : 0.630 11.310 12681 Z= 0.338 Chirality : 0.047 0.272 1402 Planarity : 0.005 0.053 1543 Dihedral : 15.332 66.673 1630 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.48 % Allowed : 16.96 % 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 (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: -0.01 (0.25), residues: 1066 helix: 1.47 (0.23), residues: 513 sheet: -1.48 (0.47), residues: 93 loop : -1.41 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 561 HIS 0.006 0.001 HIS A 323 PHE 0.016 0.002 PHE A 778 TYR 0.017 0.002 TYR A 781 ARG 0.004 0.001 ARG A 166 *********************** 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: 30 poor density : 56 time to evaluate : 0.948 Fit side-chains REVERT: A 21 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7665 (mtm) REVERT: A 85 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7550 (ptt180) REVERT: A 490 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.4804 (mtt) REVERT: A 751 PHE cc_start: 0.7444 (t80) cc_final: 0.7173 (t80) REVERT: A 756 ASP cc_start: 0.7741 (t0) cc_final: 0.7523 (t0) REVERT: A 1025 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6210 (tmm-80) REVERT: A 1084 VAL cc_start: 0.7090 (t) cc_final: 0.6730 (m) outliers start: 30 outliers final: 14 residues processed: 75 average time/residue: 1.1853 time to fit residues: 96.0584 Evaluate side-chains 72 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 622 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 0.0770 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.7144 ------------------------------------------------------------------------------- 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 = 0.110341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087902 restraints weight = 15339.426| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.96 r_work: 0.3086 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9246 Z= 0.238 Angle : 0.573 11.772 12681 Z= 0.307 Chirality : 0.043 0.253 1402 Planarity : 0.005 0.056 1543 Dihedral : 15.207 59.814 1630 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.44 % Allowed : 18.47 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.25), residues: 1066 helix: 1.62 (0.23), residues: 513 sheet: -1.46 (0.48), residues: 90 loop : -1.41 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.005 0.001 HIS A 323 PHE 0.012 0.001 PHE A 778 TYR 0.016 0.002 TYR A 989 ARG 0.002 0.000 ARG A 332 *********************** 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 79 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.963 Fit side-chains REVERT: A 196 MET cc_start: 0.8600 (ptm) cc_final: 0.8341 (ptm) REVERT: A 490 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.4767 (mtt) REVERT: A 756 ASP cc_start: 0.7796 (t0) cc_final: 0.7592 (t0) REVERT: A 1025 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6186 (tmm-80) outliers start: 21 outliers final: 12 residues processed: 74 average time/residue: 1.2200 time to fit residues: 97.3322 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 : 0.973 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 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 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.087728 restraints weight = 15268.129| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.98 r_work: 0.3076 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9246 Z= 0.254 Angle : 0.587 11.890 12681 Z= 0.314 Chirality : 0.044 0.254 1402 Planarity : 0.005 0.056 1543 Dihedral : 15.217 59.760 1630 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.44 % Allowed : 18.93 % Favored : 78.63 % 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: 1.58 (0.23), residues: 513 sheet: -1.44 (0.48), residues: 90 loop : -1.41 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.005 0.001 HIS A 323 PHE 0.012 0.001 PHE A 778 TYR 0.015 0.002 TYR A 989 ARG 0.002 0.000 ARG A 166 *********************** 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 76 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 1.028 Fit side-chains REVERT: A 85 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7640 (ptt180) REVERT: A 196 MET cc_start: 0.8637 (ptm) cc_final: 0.8351 (ptm) REVERT: A 490 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.4836 (mtt) REVERT: A 1025 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6234 (tmm-80) outliers start: 21 outliers final: 13 residues processed: 70 average time/residue: 1.2101 time to fit residues: 91.5230 Evaluate side-chains 67 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 627 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: 3.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.111254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088591 restraints weight = 15229.748| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.04 r_work: 0.3102 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9246 Z= 0.205 Angle : 0.569 12.064 12681 Z= 0.303 Chirality : 0.043 0.246 1402 Planarity : 0.004 0.055 1543 Dihedral : 15.099 59.763 1630 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.21 % Allowed : 19.51 % Favored : 78.28 % 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: 0.21 (0.25), residues: 1066 helix: 1.69 (0.23), residues: 515 sheet: -1.39 (0.48), residues: 90 loop : -1.36 (0.26), residues: 461 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 0.012 0.001 PHE A 754 TYR 0.017 0.001 TYR A 989 ARG 0.002 0.000 ARG A 37 ********************** 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 75 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.907 Fit side-chains REVERT: A 85 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7638 (ptt180) REVERT: A 196 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8333 (ptm) REVERT: A 490 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.4770 (mtt) REVERT: A 1025 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6167 (tmm-80) outliers start: 19 outliers final: 13 residues processed: 71 average time/residue: 1.1737 time to fit residues: 90.1341 Evaluate side-chains 67 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.110882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088218 restraints weight = 15195.449| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.04 r_work: 0.3094 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 0.031 9246 Z= 0.222 Angle : 0.575 12.026 12681 Z= 0.306 Chirality : 0.043 0.247 1402 Planarity : 0.004 0.054 1543 Dihedral : 15.094 59.997 1630 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.09 % Allowed : 20.09 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.25), residues: 1066 helix: 1.65 (0.23), residues: 514 sheet: -1.40 (0.49), residues: 90 loop : -1.34 (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 754 TYR 0.017 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: 4979.06 seconds wall clock time: 89 minutes 3.24 seconds (5343.24 seconds total)