Starting phenix.real_space_refine on Thu Sep 26 06:18:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/09_2024/7dte_30852.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/09_2024/7dte_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/09_2024/7dte_30852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/09_2024/7dte_30852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/09_2024/7dte_30852.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dte_30852/09_2024/7dte_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.62, per 1000 atoms: 0.63 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 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: 4.21 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: 5.05 Time building geometry restraints manager: 3.40 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: 1.940 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.340 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.390 ------------------------------------------------------------------------------- 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 : 0.006 0.049 12504 Z= 0.421 Angle : 0.606 9.592 17249 Z= 0.342 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.151 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: 1.2900 time to fit residues: 263.0666 Evaluate side-chains 139 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 12504 Z= 0.200 Angle : 0.548 8.750 17249 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 *********************** 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 fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8252 (tpt90) cc_final: 0.7892 (tpm170) REVERT: A 54 CYS cc_start: 0.7855 (t) cc_final: 0.7562 (t) REVERT: A 218 ASP cc_start: 0.7369 (t0) cc_final: 0.7163 (t0) REVERT: A 223 ILE cc_start: 0.8890 (mm) cc_final: 0.8670 (mp) REVERT: A 277 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: A 394 THR cc_start: 0.9093 (p) cc_final: 0.8891 (p) REVERT: A 450 ILE cc_start: 0.8845 (tp) cc_final: 0.8627 (tp) REVERT: A 668 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7962 (ttp) REVERT: A 825 ASP cc_start: 0.7082 (m-30) cc_final: 0.6809 (m-30) REVERT: B 62 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6244 (tmm) REVERT: B 67 MET cc_start: 0.6386 (ttt) cc_final: 0.6126 (tmm) REVERT: B 70 MET cc_start: 0.6379 (mmp) cc_final: 0.6125 (tmm) REVERT: B 104 ASN cc_start: 0.7858 (t0) cc_final: 0.7619 (t0) REVERT: B 139 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7726 (ttpt) REVERT: B 165 LYS cc_start: 0.8425 (mmtt) cc_final: 0.7774 (tttm) outliers start: 22 outliers final: 9 residues processed: 159 average time/residue: 1.2020 time to fit residues: 208.5905 Evaluate side-chains 149 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 113 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 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 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 104 ASN D 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12504 Z= 0.239 Angle : 0.535 8.054 17249 Z= 0.285 Chirality : 0.040 0.375 2005 Planarity : 0.003 0.034 1982 Dihedral : 15.148 150.583 2454 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.39 % Allowed : 12.96 % Favored : 84.65 % 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: -0.84 (0.22), residues: 1366 helix: 0.76 (0.20), residues: 693 sheet: -1.78 (0.38), residues: 142 loop : -1.98 (0.24), residues: 531 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 0.016 0.002 PHE A 694 TYR 0.016 0.001 TYR A 788 ARG 0.003 0.000 ARG A 889 *********************** 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 fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8302 (tpt90) cc_final: 0.7852 (tpm170) REVERT: A 41 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7642 (mtpt) REVERT: A 218 ASP cc_start: 0.7382 (t0) cc_final: 0.7136 (t0) REVERT: A 223 ILE cc_start: 0.8892 (mm) cc_final: 0.8649 (mt) REVERT: A 277 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: A 394 THR cc_start: 0.9075 (p) cc_final: 0.8854 (p) REVERT: A 450 ILE cc_start: 0.8877 (tp) cc_final: 0.8665 (tp) REVERT: A 522 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: A 825 ASP cc_start: 0.7141 (m-30) cc_final: 0.6884 (m-30) REVERT: B 67 MET cc_start: 0.6397 (ttt) cc_final: 0.6135 (tmm) REVERT: B 165 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7818 (tttm) REVERT: D 68 THR cc_start: 0.7963 (t) cc_final: 0.7727 (p) outliers start: 28 outliers final: 15 residues processed: 154 average time/residue: 1.1964 time to fit residues: 201.2788 Evaluate side-chains 149 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 267 LYS Chi-restraints excluded: chain A residue 277 GLU 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 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 159 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 112 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12504 Z= 0.343 Angle : 0.578 8.481 17249 Z= 0.305 Chirality : 0.042 0.167 2005 Planarity : 0.004 0.038 1982 Dihedral : 15.004 124.610 2454 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.58 % Allowed : 13.55 % Favored : 82.86 % 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: -0.65 (0.22), residues: 1366 helix: 0.83 (0.20), residues: 692 sheet: -1.46 (0.39), residues: 142 loop : -1.82 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 182 HIS 0.008 0.001 HIS A 309 PHE 0.019 0.002 PHE D 92 TYR 0.016 0.002 TYR A 149 ARG 0.004 0.000 ARG A 654 *********************** 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 173 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8305 (tpt90) cc_final: 0.8015 (tpm170) REVERT: A 41 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7770 (mtpt) REVERT: A 73 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6720 (tttp) REVERT: A 218 ASP cc_start: 0.7441 (t0) cc_final: 0.7165 (t0) REVERT: A 223 ILE cc_start: 0.8883 (mm) cc_final: 0.8633 (mt) REVERT: A 277 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: A 394 THR cc_start: 0.9071 (p) cc_final: 0.8856 (p) REVERT: A 450 ILE cc_start: 0.8943 (tp) cc_final: 0.8736 (tp) REVERT: A 825 ASP cc_start: 0.7200 (m-30) cc_final: 0.6895 (m-30) REVERT: A 902 MET cc_start: 0.7473 (mtp) cc_final: 0.7257 (mtp) REVERT: B 62 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6191 (tmm) REVERT: B 165 LYS cc_start: 0.8460 (mmtt) cc_final: 0.7817 (tttm) REVERT: D 151 SER cc_start: 0.7806 (p) cc_final: 0.7564 (t) outliers start: 42 outliers final: 16 residues processed: 157 average time/residue: 1.2097 time to fit residues: 207.4780 Evaluate side-chains 148 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 277 GLU 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 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 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 146 THR Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12504 Z= 0.245 Angle : 0.525 8.163 17249 Z= 0.278 Chirality : 0.040 0.164 2005 Planarity : 0.003 0.034 1982 Dihedral : 14.916 107.691 2454 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.50 % Allowed : 14.32 % Favored : 82.18 % 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: -0.39 (0.23), residues: 1366 helix: 1.01 (0.20), residues: 698 sheet: -1.16 (0.42), residues: 137 loop : -1.74 (0.25), residues: 531 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 0.015 0.002 PHE A 694 TYR 0.016 0.001 TYR A 788 ARG 0.003 0.000 ARG A 726 *********************** 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 175 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8313 (tpt90) cc_final: 0.7785 (tpm170) REVERT: A 41 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7781 (mtpt) REVERT: A 73 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6676 (tttp) REVERT: A 218 ASP cc_start: 0.7380 (t0) cc_final: 0.7119 (t0) REVERT: A 277 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: A 825 ASP cc_start: 0.7226 (m-30) cc_final: 0.6927 (m-30) REVERT: B 165 LYS cc_start: 0.8453 (mmtt) cc_final: 0.7823 (tttm) REVERT: D 104 ASN cc_start: 0.8201 (m-40) cc_final: 0.7988 (m-40) REVERT: D 151 SER cc_start: 0.7785 (p) cc_final: 0.7507 (t) REVERT: D 173 SER cc_start: 0.7117 (t) cc_final: 0.6814 (m) outliers start: 41 outliers final: 20 residues processed: 158 average time/residue: 1.1520 time to fit residues: 199.3339 Evaluate side-chains 153 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 259 THR Chi-restraints excluded: chain A residue 277 GLU 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 648 LEU Chi-restraints excluded: chain A residue 758 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 C residue 62 MET 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 146 THR Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 112 optimal weight: 0.0170 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 overall best weight: 1.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12504 Z= 0.239 Angle : 0.523 8.521 17249 Z= 0.275 Chirality : 0.040 0.170 2005 Planarity : 0.003 0.034 1982 Dihedral : 14.845 88.209 2454 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.15 % Allowed : 15.00 % Favored : 81.84 % 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: -0.22 (0.23), residues: 1366 helix: 1.12 (0.20), residues: 704 sheet: -1.01 (0.42), residues: 137 loop : -1.66 (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 0.016 0.002 PHE A 694 TYR 0.015 0.001 TYR A 788 ARG 0.003 0.000 ARG A 726 *********************** 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 168 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8293 (tpt90) cc_final: 0.8045 (mmm160) REVERT: A 41 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7785 (mtpt) REVERT: A 73 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6671 (tttp) REVERT: A 218 ASP cc_start: 0.7379 (t0) cc_final: 0.7107 (t0) REVERT: A 223 ILE cc_start: 0.8845 (mm) cc_final: 0.8572 (mt) REVERT: A 277 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: A 825 ASP cc_start: 0.7241 (m-30) cc_final: 0.6937 (m-30) REVERT: B 165 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7814 (tttm) REVERT: D 151 SER cc_start: 0.7764 (p) cc_final: 0.7485 (t) REVERT: D 173 SER cc_start: 0.7114 (t) cc_final: 0.6820 (m) outliers start: 37 outliers final: 18 residues processed: 154 average time/residue: 1.2070 time to fit residues: 203.0187 Evaluate side-chains 150 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 259 THR Chi-restraints excluded: chain A residue 277 GLU 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 758 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 790 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12504 Z= 0.154 Angle : 0.485 9.807 17249 Z= 0.253 Chirality : 0.038 0.160 2005 Planarity : 0.003 0.031 1982 Dihedral : 14.780 73.603 2454 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.39 % Allowed : 16.37 % Favored : 81.24 % 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: 0.08 (0.23), residues: 1366 helix: 1.37 (0.20), residues: 700 sheet: -0.86 (0.43), residues: 137 loop : -1.51 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 182 HIS 0.006 0.001 HIS A 309 PHE 0.013 0.001 PHE A 753 TYR 0.013 0.001 TYR A 788 ARG 0.008 0.000 ARG B 57 *********************** 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 162 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8238 (tpt90) cc_final: 0.8031 (mmm160) REVERT: A 41 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7761 (mtpt) REVERT: A 73 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6635 (tttp) REVERT: A 136 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: A 218 ASP cc_start: 0.7343 (t0) cc_final: 0.7077 (t0) REVERT: A 277 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: A 522 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: A 665 GLU cc_start: 0.8253 (pm20) cc_final: 0.7686 (pm20) REVERT: A 805 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 825 ASP cc_start: 0.7200 (m-30) cc_final: 0.6933 (m-30) REVERT: A 902 MET cc_start: 0.7553 (mtp) cc_final: 0.7208 (mtt) REVERT: B 105 ASN cc_start: 0.7898 (t0) cc_final: 0.7496 (m-40) REVERT: B 165 LYS cc_start: 0.8401 (mmtt) cc_final: 0.7778 (tttm) REVERT: C 43 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7743 (mmtm) REVERT: D 68 THR cc_start: 0.7991 (t) cc_final: 0.7668 (p) REVERT: D 151 SER cc_start: 0.7754 (p) cc_final: 0.7490 (t) REVERT: D 173 SER cc_start: 0.6965 (t) cc_final: 0.6682 (m) outliers start: 28 outliers final: 12 residues processed: 153 average time/residue: 1.2493 time to fit residues: 210.4739 Evaluate side-chains 149 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 HIS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 GLU 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 D residue 111 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 0.0270 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 790 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12504 Z= 0.151 Angle : 0.487 10.186 17249 Z= 0.251 Chirality : 0.038 0.157 2005 Planarity : 0.003 0.030 1982 Dihedral : 14.752 76.242 2454 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.30 % Allowed : 16.45 % Favored : 81.24 % 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: 0.22 (0.23), residues: 1366 helix: 1.47 (0.20), residues: 701 sheet: -0.76 (0.43), residues: 137 loop : -1.42 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 182 HIS 0.006 0.001 HIS A 309 PHE 0.013 0.001 PHE A 753 TYR 0.013 0.001 TYR A 788 ARG 0.006 0.000 ARG A 105 *********************** 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 164 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7655 (mtpt) REVERT: A 73 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6725 (tttp) REVERT: A 136 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: A 218 ASP cc_start: 0.7340 (t0) cc_final: 0.7088 (t0) REVERT: A 277 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: A 665 GLU cc_start: 0.8254 (pm20) cc_final: 0.7672 (pm20) REVERT: A 825 ASP cc_start: 0.7195 (m-30) cc_final: 0.6934 (m-30) REVERT: A 902 MET cc_start: 0.7468 (mtp) cc_final: 0.7123 (mtt) REVERT: B 105 ASN cc_start: 0.7892 (t0) cc_final: 0.7534 (m-40) REVERT: B 165 LYS cc_start: 0.8405 (mmtt) cc_final: 0.7821 (tttm) REVERT: D 68 THR cc_start: 0.7970 (t) cc_final: 0.7647 (p) REVERT: D 104 ASN cc_start: 0.8149 (m-40) cc_final: 0.7943 (m-40) REVERT: D 151 SER cc_start: 0.7711 (p) cc_final: 0.7423 (t) REVERT: D 173 SER cc_start: 0.6977 (t) cc_final: 0.6732 (m) outliers start: 27 outliers final: 17 residues processed: 157 average time/residue: 1.1183 time to fit residues: 192.6845 Evaluate side-chains 152 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 HIS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 GLU 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 806 THR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 30.0000 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 82 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN D 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12504 Z= 0.274 Angle : 0.541 9.655 17249 Z= 0.280 Chirality : 0.040 0.162 2005 Planarity : 0.004 0.031 1982 Dihedral : 14.736 76.470 2454 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.30 % Allowed : 16.88 % Favored : 80.82 % 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: 0.14 (0.23), residues: 1366 helix: 1.38 (0.20), residues: 694 sheet: -0.74 (0.43), residues: 137 loop : -1.42 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 598 HIS 0.014 0.001 HIS A 75 PHE 0.018 0.002 PHE A 920 TYR 0.017 0.002 TYR A 788 ARG 0.006 0.001 ARG A 105 *********************** 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 165 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7168 (mmm160) REVERT: A 41 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7695 (mtpt) REVERT: A 73 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6708 (tttp) REVERT: A 218 ASP cc_start: 0.7391 (t0) cc_final: 0.7153 (t0) REVERT: A 277 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7457 (mm-30) REVERT: A 825 ASP cc_start: 0.7231 (m-30) cc_final: 0.6947 (m-30) REVERT: A 902 MET cc_start: 0.7434 (mtp) cc_final: 0.7098 (mtt) REVERT: B 105 ASN cc_start: 0.7943 (t0) cc_final: 0.7489 (m110) REVERT: B 165 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7850 (tttm) REVERT: D 68 THR cc_start: 0.7980 (t) cc_final: 0.7657 (p) REVERT: D 104 ASN cc_start: 0.8192 (m-40) cc_final: 0.7985 (m-40) REVERT: D 173 SER cc_start: 0.6986 (t) cc_final: 0.6738 (m) outliers start: 27 outliers final: 14 residues processed: 155 average time/residue: 1.1561 time to fit residues: 196.5529 Evaluate side-chains 155 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG 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 75 HIS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 GLU 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 758 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 D residue 111 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.2980 chunk 139 optimal weight: 20.0000 chunk 128 optimal weight: 0.0170 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12504 Z= 0.185 Angle : 0.509 11.402 17249 Z= 0.263 Chirality : 0.038 0.161 2005 Planarity : 0.003 0.030 1982 Dihedral : 14.693 74.980 2454 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.79 % Allowed : 17.48 % Favored : 80.73 % 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: 0.24 (0.23), residues: 1366 helix: 1.45 (0.20), residues: 700 sheet: -0.72 (0.43), residues: 137 loop : -1.37 (0.26), residues: 529 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 0.014 0.001 PHE A 920 TYR 0.013 0.001 TYR A 788 ARG 0.006 0.000 ARG A 105 ********************** 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 154 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7214 (mmm160) REVERT: A 41 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7652 (mtpt) REVERT: A 73 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6730 (tttp) REVERT: A 218 ASP cc_start: 0.7343 (t0) cc_final: 0.7068 (t0) REVERT: A 277 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: A 665 GLU cc_start: 0.8266 (pm20) cc_final: 0.7691 (pm20) REVERT: A 825 ASP cc_start: 0.7216 (m-30) cc_final: 0.6933 (m-30) REVERT: A 902 MET cc_start: 0.7394 (mtp) cc_final: 0.7049 (mtt) REVERT: B 105 ASN cc_start: 0.7914 (t0) cc_final: 0.7467 (m110) REVERT: B 165 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7854 (tttm) REVERT: D 68 THR cc_start: 0.7986 (t) cc_final: 0.7660 (p) REVERT: D 151 SER cc_start: 0.7755 (p) cc_final: 0.7420 (t) REVERT: D 173 SER cc_start: 0.6967 (t) cc_final: 0.6760 (m) outliers start: 21 outliers final: 14 residues processed: 144 average time/residue: 1.1356 time to fit residues: 178.7301 Evaluate side-chains 149 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG 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 75 HIS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 GLU 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 758 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 D residue 111 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** 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 = 0.3677 r_free = 0.3677 target = 0.153254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104091 restraints weight = 12089.001| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.11 r_work: 0.2872 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12504 Z= 0.164 Angle : 0.499 11.140 17249 Z= 0.257 Chirality : 0.038 0.160 2005 Planarity : 0.003 0.029 1982 Dihedral : 14.635 73.641 2454 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.96 % Allowed : 17.31 % Favored : 80.73 % 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: 0.35 (0.23), residues: 1366 helix: 1.53 (0.20), residues: 702 sheet: -0.71 (0.43), residues: 137 loop : -1.29 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 598 HIS 0.009 0.001 HIS A 75 PHE 0.014 0.001 PHE A 920 TYR 0.013 0.001 TYR A 788 ARG 0.004 0.000 ARG A 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4019.72 seconds wall clock time: 71 minutes 25.69 seconds (4285.69 seconds total)