Starting phenix.real_space_refine on Wed Jul 30 12:18:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dte_30852/07_2025/7dte_30852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dte_30852/07_2025/7dte_30852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dte_30852/07_2025/7dte_30852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dte_30852/07_2025/7dte_30852.map" model { file = "/net/cci-nas-00/data/ceres_data/7dte_30852/07_2025/7dte_30852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dte_30852/07_2025/7dte_30852.cif" } resolution = 3.0 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= 0.121 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 2 6.06 5 P 62 5.49 5 S 82 5.16 5 C 7451 2.51 5 N 2062 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12130 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7473 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 897} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1401 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 554 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1387 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 693 Classifications: {'RNA': 33} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna2p': 1, 'rna3p': 31} Chain: "G" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 620 Classifications: {'RNA': 29} Modifications used: {'rna3p_pur': 16, 'rna3p_pyr': 13} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2459 SG CYS A 301 61.099 83.925 53.740 1.00 20.61 S ATOM 2500 SG CYS A 306 60.078 87.463 51.962 1.00 18.78 S ATOM 2532 SG CYS A 310 59.093 83.980 50.572 1.00 19.77 S ATOM 3940 SG CYS A 487 62.495 86.092 74.086 1.00 17.16 S ATOM 5193 SG CYS A 645 62.385 89.584 73.101 1.00 24.14 S ATOM 5199 SG CYS A 646 63.789 86.453 70.853 1.00 21.71 S Time building chain proxies: 8.13, per 1000 atoms: 0.67 Number of scatterers: 12130 At special positions: 0 Unit cell: (91.84, 131.2, 160.72, 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 2 29.99 S 82 16.00 P 62 15.00 O 2471 8.00 N 2062 7.00 C 7451 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: 3.30 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 54.7% alpha, 12.9% beta 27 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.861A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.886A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.500A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.138A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.484A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.541A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.642A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.870A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.715A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 removed outlier: 3.626A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.557A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.216A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.735A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.917A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.807A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.862A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.633A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.501A pdb=" N THR A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.910A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.691A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.998A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 915' Processing helix chain 'A' and resid 918 through 924 Processing helix chain 'B' and resid 9 through 27 removed outlier: 3.863A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 95 removed outlier: 3.945A pdb=" N LYS B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.664A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.856A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.696A pdb=" N LEU B 180 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 61 removed outlier: 4.076A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'D' and resid 10 through 27 removed outlier: 4.066A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.556A pdb=" N LEU D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.835A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.604A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.654A pdb=" N ASN D 179 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.144A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.144A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 114 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.842A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.419A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.419A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.320A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AB2, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB3, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.754A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.54 Time building geometry restraints manager: 3.90 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: 3515 1.33 - 1.45: 2487 1.45 - 1.57: 6252 1.57 - 1.69: 122 1.69 - 1.81: 128 Bond restraints: 12504 Sorted by residual: bond pdb=" C SER B 177 " pdb=" N PRO B 178 " ideal model delta sigma weight residual 1.334 1.347 -0.014 8.40e-03 1.42e+04 2.63e+00 bond pdb=" CB VAL A 605 " pdb=" CG2 VAL A 605 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.06e+00 bond pdb=" CG LEU A 731 " pdb=" CD2 LEU A 731 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" O5' A F 19 " pdb=" C5' A F 19 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.86e+00 bond pdb=" O5' G F -1 " pdb=" C5' G F -1 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.73e+00 ... (remaining 12499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 16974 1.92 - 3.84: 236 3.84 - 5.76: 34 5.76 - 7.67: 3 7.67 - 9.59: 2 Bond angle restraints: 17249 Sorted by residual: angle pdb=" N SER D 85 " pdb=" CA SER D 85 " pdb=" C SER D 85 " ideal model delta sigma weight residual 114.56 109.02 5.54 1.27e+00 6.20e-01 1.91e+01 angle pdb=" N VAL A 320 " pdb=" CA VAL A 320 " pdb=" C VAL A 320 " ideal model delta sigma weight residual 112.96 108.78 4.18 1.00e+00 1.00e+00 1.75e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 118.17 -8.36 2.21e+00 2.05e-01 1.43e+01 angle pdb=" N THR A 120 " pdb=" CA THR A 120 " pdb=" C THR A 120 " ideal model delta sigma weight residual 110.35 114.62 -4.27 1.36e+00 5.41e-01 9.86e+00 angle pdb=" O3' C F 18 " pdb=" C3' C F 18 " pdb=" C2' C F 18 " ideal model delta sigma weight residual 109.50 113.73 -4.23 1.50e+00 4.44e-01 7.96e+00 ... (remaining 17244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 7314 34.69 - 69.37: 257 69.37 - 104.06: 31 104.06 - 138.74: 0 138.74 - 173.43: 1 Dihedral angle restraints: 7603 sinusoidal: 3523 harmonic: 4080 Sorted by residual: dihedral pdb=" C4' C F 18 " pdb=" C3' C F 18 " pdb=" C2' C F 18 " pdb=" C1' C F 18 " ideal model delta sinusoidal sigma weight residual -35.00 36.58 -71.58 1 8.00e+00 1.56e-02 1.03e+02 dihedral pdb=" C5' C F 18 " pdb=" C4' C F 18 " pdb=" C3' C F 18 " pdb=" O3' C F 18 " ideal model delta sinusoidal sigma weight residual 147.00 78.93 68.07 1 8.00e+00 1.56e-02 9.40e+01 dihedral pdb=" O4' C F 18 " pdb=" C4' C F 18 " pdb=" C3' C F 18 " pdb=" C2' C F 18 " ideal model delta sinusoidal sigma weight residual 24.00 -37.31 61.31 1 8.00e+00 1.56e-02 7.80e+01 ... (remaining 7600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1647 0.055 - 0.110: 321 0.110 - 0.164: 33 0.164 - 0.219: 2 0.219 - 0.274: 2 Chirality restraints: 2005 Sorted by residual: chirality pdb=" C3' C F 18 " pdb=" C4' C F 18 " pdb=" O3' C F 18 " pdb=" C2' C F 18 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2' C F 18 " pdb=" C3' C F 18 " pdb=" O2' C F 18 " pdb=" C1' C F 18 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' G F -1 " pdb=" C4' G F -1 " pdb=" O3' G F -1 " pdb=" C2' G F -1 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2002 not shown) Planarity restraints: 1982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 118 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ARG A 118 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG A 118 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 119 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO B 178 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.02e+00 pdb=" N PRO D 183 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.028 5.00e-02 4.00e+02 ... (remaining 1979 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 86 2.57 - 3.15: 9712 3.15 - 3.73: 18923 3.73 - 4.32: 27476 4.32 - 4.90: 45052 Nonbonded interactions: 101249 Sorted by model distance: nonbonded pdb=" O2 C F 18 " pdb=" N7 A F 19 " model vdw 1.985 3.120 nonbonded pdb=" O4 U F -2 " pdb=" O6 G F -1 " model vdw 2.193 3.040 nonbonded pdb=" ND2 ASN B 43 " pdb=" O4' A F 17 " model vdw 2.204 3.120 nonbonded pdb=" ND2 ASN B 43 " pdb=" O5' A F 17 " model vdw 2.213 3.120 nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.222 3.040 ... (remaining 101244 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 18 or (resid 19 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.380 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: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 38.220 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:16.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.476 12512 Z= 0.285 Angle : 0.633 14.218 17255 Z= 0.345 Chirality : 0.043 0.274 2005 Planarity : 0.004 0.052 1982 Dihedral : 16.804 173.428 4959 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -2.94 (0.19), residues: 1366 helix: -1.06 (0.18), residues: 687 sheet: -3.08 (0.34), residues: 131 loop : -2.73 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.021 0.002 PHE A 920 TYR 0.015 0.002 TYR A 788 ARG 0.004 0.000 ARG A 914 Details of bonding type rmsd hydrogen bonds : bond 0.17230 ( 642) hydrogen bonds : angle 6.87093 ( 1798) metal coordination : bond 0.17207 ( 8) metal coordination : angle 9.82959 ( 6) covalent geometry : bond 0.00647 (12504) covalent geometry : angle 0.60579 (17249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8156 (tpt90) cc_final: 0.7949 (tpt170) REVERT: A 54 CYS cc_start: 0.8106 (t) cc_final: 0.7756 (t) REVERT: A 110 MET cc_start: 0.6997 (mmp) cc_final: 0.6718 (mmp) REVERT: A 223 ILE cc_start: 0.8847 (mm) cc_final: 0.8604 (mp) REVERT: A 450 ILE cc_start: 0.8967 (tp) cc_final: 0.8730 (tp) REVERT: A 519 MET cc_start: 0.8919 (mtp) cc_final: 0.8706 (mtt) REVERT: A 555 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7722 (mtm180) REVERT: A 825 ASP cc_start: 0.7003 (m-30) cc_final: 0.6719 (m-30) REVERT: B 67 MET cc_start: 0.6362 (ttt) cc_final: 0.6123 (tmm) REVERT: B 70 MET cc_start: 0.6791 (mmp) cc_final: 0.6423 (tmm) REVERT: B 104 ASN cc_start: 0.8050 (t0) cc_final: 0.7829 (t0) REVERT: B 139 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7705 (ttpt) REVERT: B 165 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7682 (tttm) REVERT: D 104 ASN cc_start: 0.8200 (m110) cc_final: 0.7963 (m110) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.3715 time to fit residues: 278.8522 Evaluate side-chains 139 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 30.0000 chunk 106 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 81 GLN A 99 HIS A 209 ASN A 356 ASN A 534 ASN A 613 HIS A 725 HIS A 790 ASN B 108 ASN B 140 ASN B 168 GLN C 31 GLN C 36 HIS D 100 ASN D 108 ASN D 168 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.151342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104269 restraints weight = 12238.622| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.16 r_work: 0.2846 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12512 Z= 0.140 Angle : 0.550 8.750 17255 Z= 0.293 Chirality : 0.040 0.406 2005 Planarity : 0.004 0.038 1982 Dihedral : 15.367 167.429 2454 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.88 % Allowed : 10.91 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.37 (0.22), residues: 1366 helix: 0.37 (0.20), residues: 678 sheet: -2.36 (0.36), residues: 129 loop : -2.15 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 509 HIS 0.007 0.001 HIS C 36 PHE 0.014 0.001 PHE A 694 TYR 0.013 0.001 TYR A 903 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 642) hydrogen bonds : angle 4.54414 ( 1798) metal coordination : bond 0.00969 ( 8) metal coordination : angle 2.70203 ( 6) covalent geometry : bond 0.00307 (12504) covalent geometry : angle 0.54760 (17249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8268 (tpt90) cc_final: 0.7869 (tpm170) REVERT: A 54 CYS cc_start: 0.8309 (t) cc_final: 0.7994 (t) REVERT: A 110 MET cc_start: 0.7447 (mmp) cc_final: 0.7156 (mmm) REVERT: A 223 ILE cc_start: 0.8947 (mm) cc_final: 0.8692 (mp) REVERT: A 277 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8234 (mm-30) REVERT: A 394 THR cc_start: 0.9216 (p) cc_final: 0.8996 (p) REVERT: A 450 ILE cc_start: 0.8939 (tp) cc_final: 0.8721 (tp) REVERT: A 668 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8448 (ttp) REVERT: A 811 GLU cc_start: 0.8587 (tt0) cc_final: 0.8342 (tt0) REVERT: A 825 ASP cc_start: 0.7541 (m-30) cc_final: 0.7165 (m-30) REVERT: A 855 MET cc_start: 0.6945 (mmt) cc_final: 0.6722 (mmm) REVERT: B 62 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6661 (tmm) REVERT: B 67 MET cc_start: 0.6153 (ttt) cc_final: 0.5377 (tmm) REVERT: B 70 MET cc_start: 0.6654 (mmp) cc_final: 0.5923 (tmm) REVERT: B 104 ASN cc_start: 0.8219 (t0) cc_final: 0.7929 (t0) REVERT: B 139 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7938 (ttpt) REVERT: B 165 LYS cc_start: 0.8573 (mmtt) cc_final: 0.7743 (tttm) REVERT: D 104 ASN cc_start: 0.8307 (m110) cc_final: 0.8107 (m110) REVERT: D 134 ASP cc_start: 0.7068 (t0) cc_final: 0.6822 (t0) REVERT: D 189 LEU cc_start: 0.8483 (mp) cc_final: 0.8273 (mm) outliers start: 22 outliers final: 9 residues processed: 159 average time/residue: 1.2448 time to fit residues: 215.9020 Evaluate side-chains 149 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 138 optimal weight: 50.0000 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 875 GLN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.097368 restraints weight = 12474.552| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.17 r_work: 0.2773 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12512 Z= 0.260 Angle : 0.621 8.744 17255 Z= 0.328 Chirality : 0.044 0.351 2005 Planarity : 0.004 0.039 1982 Dihedral : 15.193 146.253 2454 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.73 % Allowed : 13.13 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.04 (0.22), residues: 1366 helix: 0.52 (0.20), residues: 705 sheet: -1.91 (0.38), residues: 133 loop : -2.02 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 182 HIS 0.008 0.001 HIS A 309 PHE 0.023 0.002 PHE D 92 TYR 0.016 0.002 TYR A 788 ARG 0.004 0.001 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.05688 ( 642) hydrogen bonds : angle 4.46137 ( 1798) metal coordination : bond 0.00842 ( 8) metal coordination : angle 2.58348 ( 6) covalent geometry : bond 0.00625 (12504) covalent geometry : angle 0.61940 (17249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8335 (tpt90) cc_final: 0.8026 (tpm170) REVERT: A 41 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7708 (mtpt) REVERT: A 54 CYS cc_start: 0.8236 (t) cc_final: 0.7965 (t) REVERT: A 73 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7014 (ttpp) REVERT: A 92 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7193 (p0) REVERT: A 223 ILE cc_start: 0.8959 (mm) cc_final: 0.8719 (mt) REVERT: A 315 VAL cc_start: 0.9002 (p) cc_final: 0.8690 (m) REVERT: A 394 THR cc_start: 0.9204 (p) cc_final: 0.8949 (p) REVERT: A 450 ILE cc_start: 0.9040 (tp) cc_final: 0.8828 (tp) REVERT: A 668 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8641 (ttp) REVERT: A 825 ASP cc_start: 0.7619 (m-30) cc_final: 0.7224 (m-30) REVERT: A 855 MET cc_start: 0.7146 (mmt) cc_final: 0.6901 (mmm) REVERT: A 902 MET cc_start: 0.7739 (mtp) cc_final: 0.7464 (mtp) REVERT: B 67 MET cc_start: 0.6216 (ttt) cc_final: 0.5526 (ppp) REVERT: B 70 MET cc_start: 0.6693 (mmp) cc_final: 0.6053 (tmm) REVERT: B 104 ASN cc_start: 0.8193 (t0) cc_final: 0.7935 (t0) REVERT: B 139 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7950 (ttpt) REVERT: B 165 LYS cc_start: 0.8632 (mmtt) cc_final: 0.7781 (tttm) REVERT: D 58 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7706 (tmmt) REVERT: D 104 ASN cc_start: 0.8504 (m110) cc_final: 0.8269 (m110) outliers start: 32 outliers final: 15 residues processed: 154 average time/residue: 1.2717 time to fit residues: 213.3604 Evaluate side-chains 148 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.0270 chunk 75 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.149653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.101549 restraints weight = 12185.794| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.13 r_work: 0.2827 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12512 Z= 0.169 Angle : 0.534 8.207 17255 Z= 0.282 Chirality : 0.040 0.169 2005 Planarity : 0.004 0.037 1982 Dihedral : 14.973 119.664 2454 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.50 % Allowed : 13.73 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.59 (0.23), residues: 1366 helix: 0.89 (0.20), residues: 702 sheet: -1.38 (0.40), residues: 137 loop : -1.88 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 598 HIS 0.007 0.001 HIS A 309 PHE 0.016 0.002 PHE A 694 TYR 0.016 0.001 TYR A 788 ARG 0.003 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 642) hydrogen bonds : angle 4.14272 ( 1798) metal coordination : bond 0.00595 ( 8) metal coordination : angle 2.11319 ( 6) covalent geometry : bond 0.00396 (12504) covalent geometry : angle 0.53275 (17249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8297 (tpt90) cc_final: 0.8015 (mmm160) REVERT: A 41 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7733 (mtpt) REVERT: A 73 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6778 (tttp) REVERT: A 110 MET cc_start: 0.7680 (mmm) cc_final: 0.7394 (mmm) REVERT: A 223 ILE cc_start: 0.8941 (mm) cc_final: 0.8677 (mt) REVERT: A 394 THR cc_start: 0.9210 (p) cc_final: 0.8988 (p) REVERT: A 522 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: A 811 GLU cc_start: 0.8510 (tt0) cc_final: 0.8293 (tt0) REVERT: A 825 ASP cc_start: 0.7609 (m-30) cc_final: 0.7221 (m-30) REVERT: A 855 MET cc_start: 0.7014 (mmt) cc_final: 0.6764 (mmm) REVERT: A 902 MET cc_start: 0.7798 (mtp) cc_final: 0.7548 (mtp) REVERT: B 62 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6585 (tmm) REVERT: B 67 MET cc_start: 0.6151 (ttt) cc_final: 0.5485 (ppp) REVERT: B 70 MET cc_start: 0.6660 (mmp) cc_final: 0.6054 (tmm) REVERT: B 165 LYS cc_start: 0.8619 (mmtt) cc_final: 0.7779 (tttm) REVERT: D 94 MET cc_start: 0.8880 (ptm) cc_final: 0.8651 (mtp) REVERT: D 104 ASN cc_start: 0.8408 (m110) cc_final: 0.8172 (m-40) outliers start: 41 outliers final: 16 residues processed: 159 average time/residue: 1.2121 time to fit residues: 211.0503 Evaluate side-chains 150 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 129 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.148215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.099229 restraints weight = 12230.977| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.15 r_work: 0.2801 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12512 Z= 0.178 Angle : 0.535 8.260 17255 Z= 0.283 Chirality : 0.040 0.168 2005 Planarity : 0.004 0.036 1982 Dihedral : 14.918 95.759 2454 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.32 % Allowed : 14.41 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.41 (0.23), residues: 1366 helix: 1.00 (0.20), residues: 704 sheet: -1.16 (0.42), residues: 137 loop : -1.79 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 598 HIS 0.007 0.001 HIS A 309 PHE 0.018 0.002 PHE A 920 TYR 0.015 0.002 TYR A 788 ARG 0.003 0.000 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 642) hydrogen bonds : angle 4.09306 ( 1798) metal coordination : bond 0.00566 ( 8) metal coordination : angle 1.92121 ( 6) covalent geometry : bond 0.00421 (12504) covalent geometry : angle 0.53423 (17249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8342 (tpt90) cc_final: 0.8015 (tpm170) REVERT: A 41 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7734 (mtpt) REVERT: A 73 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6778 (tttp) REVERT: A 110 MET cc_start: 0.7667 (mmm) cc_final: 0.7364 (mmm) REVERT: A 223 ILE cc_start: 0.8904 (mm) cc_final: 0.8617 (mt) REVERT: A 522 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: A 811 GLU cc_start: 0.8534 (tt0) cc_final: 0.8317 (tt0) REVERT: A 825 ASP cc_start: 0.7658 (m-30) cc_final: 0.7262 (m-30) REVERT: A 855 MET cc_start: 0.7070 (mmt) cc_final: 0.6839 (mmm) REVERT: B 62 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6583 (tmm) REVERT: B 67 MET cc_start: 0.6192 (ttt) cc_final: 0.5482 (ppp) REVERT: B 70 MET cc_start: 0.6615 (mmp) cc_final: 0.6047 (tmm) REVERT: B 165 LYS cc_start: 0.8615 (mmtt) cc_final: 0.7767 (tttm) REVERT: D 104 ASN cc_start: 0.8415 (m110) cc_final: 0.8204 (m-40) REVERT: D 151 SER cc_start: 0.7902 (p) cc_final: 0.7651 (t) outliers start: 39 outliers final: 20 residues processed: 158 average time/residue: 1.2044 time to fit residues: 207.7106 Evaluate side-chains 154 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 112 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 108 optimal weight: 0.0030 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 138 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.102233 restraints weight = 12373.431| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.16 r_work: 0.2849 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12512 Z= 0.144 Angle : 0.500 8.521 17255 Z= 0.264 Chirality : 0.039 0.164 2005 Planarity : 0.003 0.035 1982 Dihedral : 14.871 73.724 2454 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.07 % Allowed : 15.17 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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 (0.23), residues: 1366 helix: 1.15 (0.20), residues: 704 sheet: -1.10 (0.42), residues: 137 loop : -1.64 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 598 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.001 PHE A 694 TYR 0.015 0.001 TYR A 788 ARG 0.003 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 642) hydrogen bonds : angle 3.96408 ( 1798) metal coordination : bond 0.00495 ( 8) metal coordination : angle 1.73692 ( 6) covalent geometry : bond 0.00332 (12504) covalent geometry : angle 0.49937 (17249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8354 (tpt90) cc_final: 0.8110 (mmm160) REVERT: A 41 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7799 (mtpt) REVERT: A 73 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6854 (tttp) REVERT: A 110 MET cc_start: 0.7729 (mmm) cc_final: 0.7409 (mmm) REVERT: A 223 ILE cc_start: 0.8890 (mm) cc_final: 0.8617 (mt) REVERT: A 522 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: A 665 GLU cc_start: 0.8544 (pm20) cc_final: 0.7900 (pm20) REVERT: A 825 ASP cc_start: 0.7702 (m-30) cc_final: 0.7356 (m-30) REVERT: A 899 MET cc_start: 0.8410 (tpp) cc_final: 0.8062 (mmt) REVERT: A 902 MET cc_start: 0.7732 (mtp) cc_final: 0.7331 (mtt) REVERT: B 62 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6604 (tmm) REVERT: B 67 MET cc_start: 0.6278 (ttt) cc_final: 0.5484 (tmm) REVERT: B 70 MET cc_start: 0.6602 (mmp) cc_final: 0.6112 (tmm) REVERT: B 165 LYS cc_start: 0.8615 (mmtt) cc_final: 0.7886 (tttm) REVERT: C 43 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7920 (mmtm) REVERT: D 151 SER cc_start: 0.7987 (p) cc_final: 0.7679 (t) outliers start: 36 outliers final: 17 residues processed: 161 average time/residue: 1.2604 time to fit residues: 221.1577 Evaluate side-chains 150 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.0570 chunk 47 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.153496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105107 restraints weight = 12190.799| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.15 r_work: 0.2880 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12512 Z= 0.104 Angle : 0.471 9.506 17255 Z= 0.248 Chirality : 0.037 0.168 2005 Planarity : 0.003 0.032 1982 Dihedral : 14.816 73.623 2454 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.47 % Allowed : 16.54 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: 0.03 (0.23), residues: 1366 helix: 1.31 (0.20), residues: 712 sheet: -1.00 (0.42), residues: 137 loop : -1.52 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 182 HIS 0.015 0.001 HIS A 75 PHE 0.012 0.001 PHE A 920 TYR 0.013 0.001 TYR A 831 ARG 0.004 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 642) hydrogen bonds : angle 3.80676 ( 1798) metal coordination : bond 0.00371 ( 8) metal coordination : angle 1.51921 ( 6) covalent geometry : bond 0.00220 (12504) covalent geometry : angle 0.47030 (17249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8267 (tpt90) cc_final: 0.8039 (mmm160) REVERT: A 41 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7726 (mtpt) REVERT: A 73 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6859 (tttp) REVERT: A 110 MET cc_start: 0.7727 (mmm) cc_final: 0.7318 (mmm) REVERT: A 136 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: A 522 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: A 665 GLU cc_start: 0.8549 (pm20) cc_final: 0.7840 (pm20) REVERT: A 805 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 825 ASP cc_start: 0.7600 (m-30) cc_final: 0.7245 (m-30) REVERT: A 902 MET cc_start: 0.7585 (mtp) cc_final: 0.7180 (mtt) REVERT: B 67 MET cc_start: 0.6373 (ttt) cc_final: 0.5463 (tmm) REVERT: B 70 MET cc_start: 0.6514 (mmp) cc_final: 0.6065 (tmm) REVERT: B 105 ASN cc_start: 0.8053 (t0) cc_final: 0.7475 (m-40) REVERT: B 165 LYS cc_start: 0.8560 (mmtt) cc_final: 0.7728 (tttm) REVERT: C 43 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7797 (mmtm) REVERT: D 40 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5869 (mmpt) REVERT: D 68 THR cc_start: 0.7924 (t) cc_final: 0.7589 (p) REVERT: D 104 ASN cc_start: 0.8158 (m-40) cc_final: 0.7646 (m-40) REVERT: D 151 SER cc_start: 0.7850 (p) cc_final: 0.7542 (t) outliers start: 29 outliers final: 14 residues processed: 162 average time/residue: 1.2322 time to fit residues: 218.4778 Evaluate side-chains 154 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 119 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.151372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.103559 restraints weight = 12271.870| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.09 r_work: 0.2842 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12512 Z= 0.144 Angle : 0.515 10.725 17255 Z= 0.266 Chirality : 0.039 0.162 2005 Planarity : 0.003 0.033 1982 Dihedral : 14.781 73.688 2454 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.64 % Allowed : 16.88 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.10 (0.23), residues: 1366 helix: 1.37 (0.20), residues: 696 sheet: -0.91 (0.42), residues: 137 loop : -1.44 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 598 HIS 0.007 0.001 HIS A 309 PHE 0.017 0.001 PHE A 920 TYR 0.015 0.001 TYR A 788 ARG 0.003 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 642) hydrogen bonds : angle 3.88654 ( 1798) metal coordination : bond 0.00435 ( 8) metal coordination : angle 1.55371 ( 6) covalent geometry : bond 0.00335 (12504) covalent geometry : angle 0.51464 (17249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8313 (tpt90) cc_final: 0.8091 (mmm160) REVERT: A 41 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7764 (mtpt) REVERT: A 73 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6876 (tttp) REVERT: A 110 MET cc_start: 0.7726 (mmm) cc_final: 0.7339 (mmm) REVERT: A 665 GLU cc_start: 0.8558 (pm20) cc_final: 0.7897 (pm20) REVERT: A 805 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8627 (mp) REVERT: A 825 ASP cc_start: 0.7659 (m-30) cc_final: 0.7316 (m-30) REVERT: A 902 MET cc_start: 0.7611 (mtp) cc_final: 0.7202 (mtt) REVERT: B 67 MET cc_start: 0.6481 (ttt) cc_final: 0.5604 (tmm) REVERT: B 70 MET cc_start: 0.6629 (mmp) cc_final: 0.6081 (tmm) REVERT: B 101 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7451 (t0) REVERT: B 105 ASN cc_start: 0.8153 (t0) cc_final: 0.7547 (m110) REVERT: B 165 LYS cc_start: 0.8622 (mmtt) cc_final: 0.7882 (tttm) REVERT: C 43 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7909 (mmtm) REVERT: D 68 THR cc_start: 0.8007 (t) cc_final: 0.7685 (p) REVERT: D 151 SER cc_start: 0.7956 (p) cc_final: 0.7619 (t) outliers start: 31 outliers final: 19 residues processed: 158 average time/residue: 1.1543 time to fit residues: 199.3742 Evaluate side-chains 159 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.102249 restraints weight = 12200.690| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.11 r_work: 0.2834 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12512 Z= 0.143 Angle : 0.512 9.636 17255 Z= 0.265 Chirality : 0.039 0.163 2005 Planarity : 0.003 0.032 1982 Dihedral : 14.700 73.724 2454 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.47 % Allowed : 17.39 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: 0.15 (0.23), residues: 1366 helix: 1.38 (0.20), residues: 696 sheet: -0.83 (0.43), residues: 137 loop : -1.37 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 598 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.001 PHE A 920 TYR 0.015 0.001 TYR A 788 ARG 0.004 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 642) hydrogen bonds : angle 3.88444 ( 1798) metal coordination : bond 0.00459 ( 8) metal coordination : angle 1.64555 ( 6) covalent geometry : bond 0.00333 (12504) covalent geometry : angle 0.51083 (17249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8289 (tpt90) cc_final: 0.8049 (mmm160) REVERT: A 41 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7740 (mtpt) REVERT: A 92 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7307 (p0) REVERT: A 110 MET cc_start: 0.7741 (mmm) cc_final: 0.7395 (mmm) REVERT: A 411 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8637 (mtpm) REVERT: A 665 GLU cc_start: 0.8610 (pm20) cc_final: 0.7919 (pm20) REVERT: A 805 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 825 ASP cc_start: 0.7628 (m-30) cc_final: 0.7271 (m-30) REVERT: A 902 MET cc_start: 0.7605 (mtp) cc_final: 0.7243 (mtt) REVERT: A 906 MET cc_start: 0.7288 (mmm) cc_final: 0.6047 (tpp) REVERT: B 67 MET cc_start: 0.6406 (ttt) cc_final: 0.5642 (ppp) REVERT: B 70 MET cc_start: 0.6573 (mmp) cc_final: 0.6011 (tmm) REVERT: B 105 ASN cc_start: 0.8148 (t0) cc_final: 0.7527 (m110) REVERT: B 165 LYS cc_start: 0.8614 (mmtt) cc_final: 0.7815 (tttm) REVERT: C 43 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7920 (mmtm) REVERT: D 68 THR cc_start: 0.7938 (t) cc_final: 0.7604 (p) outliers start: 29 outliers final: 19 residues processed: 154 average time/residue: 1.2336 time to fit residues: 207.4679 Evaluate side-chains 155 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.103300 restraints weight = 12168.450| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.15 r_work: 0.2823 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12512 Z= 0.155 Angle : 0.524 9.364 17255 Z= 0.272 Chirality : 0.039 0.156 2005 Planarity : 0.003 0.032 1982 Dihedral : 14.636 73.757 2454 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.13 % Allowed : 17.39 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: 0.15 (0.23), residues: 1366 helix: 1.37 (0.20), residues: 696 sheet: -0.84 (0.43), residues: 137 loop : -1.35 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 598 HIS 0.007 0.001 HIS A 309 PHE 0.017 0.002 PHE A 920 TYR 0.016 0.001 TYR A 788 ARG 0.004 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 642) hydrogen bonds : angle 3.91128 ( 1798) metal coordination : bond 0.00468 ( 8) metal coordination : angle 1.61985 ( 6) covalent geometry : bond 0.00366 (12504) covalent geometry : angle 0.52355 (17249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8314 (tpt90) cc_final: 0.8087 (mmm160) REVERT: A 41 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7701 (mtpt) REVERT: A 92 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7367 (p0) REVERT: A 110 MET cc_start: 0.7737 (mmm) cc_final: 0.7405 (mmm) REVERT: A 411 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8633 (mtpm) REVERT: A 629 MET cc_start: 0.9070 (mmm) cc_final: 0.8845 (mmp) REVERT: A 665 GLU cc_start: 0.8596 (pm20) cc_final: 0.7935 (pm20) REVERT: A 805 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8629 (mp) REVERT: A 825 ASP cc_start: 0.7662 (m-30) cc_final: 0.7316 (m-30) REVERT: A 902 MET cc_start: 0.7632 (mtp) cc_final: 0.7304 (mtt) REVERT: B 64 ASP cc_start: 0.5850 (t0) cc_final: 0.5263 (t0) REVERT: B 67 MET cc_start: 0.6504 (ttt) cc_final: 0.5741 (ppp) REVERT: B 70 MET cc_start: 0.6628 (mmp) cc_final: 0.6069 (tmm) REVERT: B 105 ASN cc_start: 0.8174 (t0) cc_final: 0.7574 (m110) REVERT: B 165 LYS cc_start: 0.8635 (mmtt) cc_final: 0.7899 (tttm) REVERT: C 43 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7991 (mmtm) REVERT: D 68 THR cc_start: 0.8036 (t) cc_final: 0.7709 (p) REVERT: D 151 SER cc_start: 0.8020 (p) cc_final: 0.7799 (p) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 1.7270 time to fit residues: 288.2840 Evaluate side-chains 155 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 0.0070 chunk 87 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.106078 restraints weight = 12172.829| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.09 r_work: 0.2878 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12512 Z= 0.112 Angle : 0.496 12.220 17255 Z= 0.256 Chirality : 0.038 0.160 2005 Planarity : 0.003 0.031 1982 Dihedral : 14.523 73.626 2454 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.96 % Allowed : 17.73 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.34 (0.23), residues: 1366 helix: 1.53 (0.20), residues: 701 sheet: -0.79 (0.42), residues: 137 loop : -1.28 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 182 HIS 0.007 0.001 HIS A 309 PHE 0.013 0.001 PHE A 753 TYR 0.013 0.001 TYR A 788 ARG 0.004 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 642) hydrogen bonds : angle 3.77321 ( 1798) metal coordination : bond 0.00387 ( 8) metal coordination : angle 1.49982 ( 6) covalent geometry : bond 0.00247 (12504) covalent geometry : angle 0.49560 (17249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9156.55 seconds wall clock time: 159 minutes 2.78 seconds (9542.78 seconds total)