Starting phenix.real_space_refine on Tue Jul 29 14:14:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yyt_11007/07_2025/6yyt_11007_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yyt_11007/07_2025/6yyt_11007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yyt_11007/07_2025/6yyt_11007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yyt_11007/07_2025/6yyt_11007.map" model { file = "/net/cci-nas-00/data/ceres_data/6yyt_11007/07_2025/6yyt_11007_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yyt_11007/07_2025/6yyt_11007_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.974 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 54 5.49 5 S 77 5.16 5 C 7014 2.51 5 N 1926 2.21 5 O 2302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 11375 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6880 Classifications: {'peptide': 853} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 824} Chain breaks: 2 Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1393 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} 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: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1391 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 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': 2} Unresolved non-hydrogen planarities: 48 Chain: "P" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13} Chain: "Q" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna3p': 11} Chain: "U" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13} 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 1864 SG CYS A 301 92.661 65.587 45.161 1.00 25.99 S ATOM 1905 SG CYS A 306 92.937 64.791 41.187 1.00 25.44 S ATOM 1937 SG CYS A 310 95.767 64.736 44.077 1.00 24.45 S ATOM 3345 SG CYS A 487 75.166 60.156 53.972 1.00 21.81 S ATOM 4598 SG CYS A 645 73.794 60.060 50.132 1.00 27.45 S ATOM 4604 SG CYS A 646 77.157 61.975 51.989 1.00 24.88 S Time building chain proxies: 8.41, per 1000 atoms: 0.74 Number of scatterers: 11375 At special positions: 0 Unit cell: (140.112, 92.574, 127.602, 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 77 16.00 P 54 15.00 O 2302 8.00 N 1926 7.00 C 7014 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: 3.14 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 57.6% alpha, 10.2% beta 22 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 78 through 90 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 159 Processing helix chain 'A' and resid 170 through 198 removed outlier: 4.013A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.553A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 3.710A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.251A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.712A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.606A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.685A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.514A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.768A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.542A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.927A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.879A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.869A 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 removed outlier: 3.740A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.555A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 847 through 852 removed outlier: 4.152A pdb=" N ASP A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 867 removed outlier: 4.058A pdb=" N ARG A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.555A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.914A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.767A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.322A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.817A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 98 removed outlier: 3.560A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.700A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.905A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.621A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.230A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 removed outlier: 3.713A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.299A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.601A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.051A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.040A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 559 removed outlier: 4.111A pdb=" N MET A 542 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA6, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AA7, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.735A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3189 1.33 - 1.45: 2214 1.45 - 1.57: 6087 1.57 - 1.69: 102 1.69 - 1.81: 122 Bond restraints: 11714 Sorted by residual: bond pdb=" O3' G T 13 " pdb=" P C T 14 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.93e+00 bond pdb=" O3' A P 17 " pdb=" P G P 18 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.50e-02 4.44e+03 6.35e+00 bond pdb=" O3' C T 14 " pdb=" P G T 15 " ideal model delta sigma weight residual 1.607 1.574 0.033 1.50e-02 4.44e+03 4.94e+00 bond pdb=" O3' U P 16 " pdb=" P A P 17 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.50e-02 4.44e+03 4.39e+00 bond pdb=" O3' G P 15 " pdb=" P U P 16 " ideal model delta sigma weight residual 1.607 1.580 0.027 1.50e-02 4.44e+03 3.29e+00 ... (remaining 11709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 15600 1.11 - 2.22: 420 2.22 - 3.33: 78 3.33 - 4.44: 34 4.44 - 5.55: 6 Bond angle restraints: 16138 Sorted by residual: angle pdb=" C3' G T 8 " pdb=" C2' G T 8 " pdb=" O2' G T 8 " ideal model delta sigma weight residual 110.70 105.54 5.16 1.50e+00 4.44e-01 1.18e+01 angle pdb=" O3' G P 8 " pdb=" C3' G P 8 " pdb=" C2' G P 8 " ideal model delta sigma weight residual 113.70 109.02 4.68 1.50e+00 4.44e-01 9.72e+00 angle pdb=" C3' A T 11 " pdb=" C2' A T 11 " pdb=" O2' A T 11 " ideal model delta sigma weight residual 110.70 115.34 -4.64 1.50e+00 4.44e-01 9.59e+00 angle pdb=" O3' G T 8 " pdb=" C3' G T 8 " pdb=" C2' G T 8 " ideal model delta sigma weight residual 113.70 109.22 4.48 1.50e+00 4.44e-01 8.90e+00 angle pdb=" O3' G P 18 " pdb=" C3' G P 18 " pdb=" C2' G P 18 " ideal model delta sigma weight residual 109.50 113.86 -4.36 1.50e+00 4.44e-01 8.46e+00 ... (remaining 16133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6178 17.91 - 35.82: 660 35.82 - 53.73: 191 53.73 - 71.63: 67 71.63 - 89.54: 21 Dihedral angle restraints: 7117 sinusoidal: 3260 harmonic: 3857 Sorted by residual: dihedral pdb=" C5' G P 18 " pdb=" C4' G P 18 " pdb=" C3' G P 18 " pdb=" O3' G P 18 " ideal model delta sinusoidal sigma weight residual 147.00 125.28 21.72 1 8.00e+00 1.56e-02 1.07e+01 dihedral pdb=" CB GLU B 48 " pdb=" CG GLU B 48 " pdb=" CD GLU B 48 " pdb=" OE1 GLU B 48 " ideal model delta sinusoidal sigma weight residual 0.00 89.54 -89.54 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 640 " pdb=" CD ARG A 640 " pdb=" NE ARG A 640 " pdb=" CZ ARG A 640 " ideal model delta sinusoidal sigma weight residual 90.00 131.86 -41.86 2 1.50e+01 4.44e-03 9.50e+00 ... (remaining 7114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1588 0.048 - 0.096: 200 0.096 - 0.145: 74 0.145 - 0.193: 11 0.193 - 0.241: 4 Chirality restraints: 1877 Sorted by residual: chirality pdb=" C3' G P 8 " pdb=" C4' G P 8 " pdb=" O3' G P 8 " pdb=" C2' G P 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3' G P 18 " pdb=" C4' G P 18 " pdb=" O3' G P 18 " pdb=" C2' G P 18 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2' A T 11 " pdb=" C3' A T 11 " pdb=" O2' A T 11 " pdb=" C1' A T 11 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1874 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G T 13 " -0.019 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 G T 13 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G T 13 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G T 13 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G T 13 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G T 13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G T 13 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G T 13 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G T 13 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G T 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G P 18 " 0.022 2.00e-02 2.50e+03 9.04e-03 2.45e+00 pdb=" N9 G P 18 " -0.017 2.00e-02 2.50e+03 pdb=" C8 G P 18 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G P 18 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G P 18 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G P 18 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G P 18 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G P 18 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G P 18 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G P 18 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G P 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G P 18 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C P 12 " 0.019 2.00e-02 2.50e+03 9.49e-03 2.03e+00 pdb=" N1 C P 12 " -0.018 2.00e-02 2.50e+03 pdb=" C2 C P 12 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C P 12 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C P 12 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C P 12 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C P 12 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C P 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C P 12 " -0.007 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2698 2.79 - 3.31: 10547 3.31 - 3.84: 19707 3.84 - 4.37: 23335 4.37 - 4.90: 38279 Nonbonded interactions: 94566 Sorted by model distance: nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.258 3.040 nonbonded pdb=" O GLY A 852 " pdb=" OG1 THR A 853 " model vdw 2.275 3.040 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.347 3.040 nonbonded pdb=" O ASN A 705 " pdb=" OG SER A 709 " model vdw 2.365 3.040 nonbonded pdb=" O ALA A 448 " pdb=" OG SER A 451 " model vdw 2.372 3.040 ... (remaining 94561 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 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)) } ncs_group { reference = (chain 'P' and resid 7 through 18) selection = (chain 'Q' and resid 7 through 18) selection = chain 'T' selection = (chain 'U' and resid 7 through 18) } 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: 90.890 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.210 Find NCS groups from input model: 0.270 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:14.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.003 0.236 11722 Z= 0.153 Angle : 0.570 25.705 16144 Z= 0.283 Chirality : 0.040 0.241 1877 Planarity : 0.002 0.033 1862 Dihedral : 16.992 89.542 4617 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.36 % Allowed : 6.14 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.98 (0.21), residues: 1286 helix: -0.06 (0.19), residues: 652 sheet: -0.62 (0.47), residues: 108 loop : -1.31 (0.23), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 82 PHE 0.010 0.001 PHE A 741 TYR 0.013 0.001 TYR A 788 ARG 0.008 0.001 ARG A 836 Details of bonding type rmsd hydrogen bonds : bond 0.13011 ( 627) hydrogen bonds : angle 5.22944 ( 1726) metal coordination : bond 0.08428 ( 8) metal coordination : angle 16.70365 ( 6) covalent geometry : bond 0.00259 (11714) covalent geometry : angle 0.47097 (16138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 1.141 Fit side-chains REVERT: B 79 LYS cc_start: 0.6908 (mmtp) cc_final: 0.6415 (ptpt) REVERT: B 85 SER cc_start: 0.8006 (p) cc_final: 0.7791 (t) outliers start: 4 outliers final: 1 residues processed: 178 average time/residue: 1.1412 time to fit residues: 222.8298 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 177 ASN A 347 HIS A 439 HIS A 570 GLN B 88 GLN B 140 ASN D 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.140115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096389 restraints weight = 16188.945| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.96 r_work: 0.3106 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11722 Z= 0.224 Angle : 0.556 6.630 16144 Z= 0.286 Chirality : 0.041 0.156 1877 Planarity : 0.004 0.070 1862 Dihedral : 14.140 74.901 2251 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.71 % Allowed : 13.27 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.11 (0.22), residues: 1286 helix: 1.07 (0.20), residues: 660 sheet: -0.65 (0.47), residues: 115 loop : -1.03 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.020 0.002 PHE A 920 TYR 0.019 0.002 TYR B 135 ARG 0.006 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 627) hydrogen bonds : angle 3.82030 ( 1726) metal coordination : bond 0.01478 ( 8) metal coordination : angle 2.77022 ( 6) covalent geometry : bond 0.00521 (11714) covalent geometry : angle 0.55318 (16138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.149 Fit side-chains REVERT: A 33 ARG cc_start: 0.6929 (mtm110) cc_final: 0.6711 (mtm110) REVERT: A 119 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6195 (tp) REVERT: A 284 ASP cc_start: 0.8497 (m-30) cc_final: 0.8279 (t0) REVERT: A 418 ASP cc_start: 0.8669 (m-30) cc_final: 0.8434 (t0) REVERT: A 552 ASN cc_start: 0.8409 (p0) cc_final: 0.8192 (p0) REVERT: A 722 ASN cc_start: 0.7864 (m110) cc_final: 0.7572 (m-40) REVERT: A 899 MET cc_start: 0.7590 (mmm) cc_final: 0.7101 (mmt) REVERT: B 79 LYS cc_start: 0.6186 (mmtp) cc_final: 0.5405 (ptpt) REVERT: B 108 ASN cc_start: 0.6924 (m-40) cc_final: 0.6694 (m-40) REVERT: C 34 GLN cc_start: 0.8317 (tp40) cc_final: 0.8027 (tp40) REVERT: D 189 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8903 (mm) outliers start: 30 outliers final: 13 residues processed: 159 average time/residue: 1.0877 time to fit residues: 189.4912 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 112 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.142232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097783 restraints weight = 16458.061| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.31 r_work: 0.3140 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11722 Z= 0.109 Angle : 0.466 6.060 16144 Z= 0.241 Chirality : 0.037 0.157 1877 Planarity : 0.003 0.052 1862 Dihedral : 14.144 76.118 2249 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.44 % Allowed : 15.43 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.73 (0.23), residues: 1286 helix: 1.55 (0.20), residues: 660 sheet: -0.38 (0.49), residues: 105 loop : -0.68 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.020 0.001 PHE A 920 TYR 0.012 0.001 TYR A 788 ARG 0.002 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 627) hydrogen bonds : angle 3.61284 ( 1726) metal coordination : bond 0.00416 ( 8) metal coordination : angle 2.16744 ( 6) covalent geometry : bond 0.00241 (11714) covalent geometry : angle 0.46454 (16138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.169 Fit side-chains REVERT: A 33 ARG cc_start: 0.6900 (mtm110) cc_final: 0.6667 (mtm110) REVERT: A 284 ASP cc_start: 0.8547 (m-30) cc_final: 0.8292 (t0) REVERT: A 418 ASP cc_start: 0.8617 (m-30) cc_final: 0.8392 (t0) REVERT: A 552 ASN cc_start: 0.8526 (p0) cc_final: 0.8305 (p0) REVERT: B 79 LYS cc_start: 0.6071 (mmtp) cc_final: 0.5356 (ptpt) REVERT: B 90 MET cc_start: 0.7565 (ttp) cc_final: 0.7331 (tmm) REVERT: C 34 GLN cc_start: 0.8303 (tp40) cc_final: 0.8037 (tp40) REVERT: D 189 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8931 (mm) outliers start: 27 outliers final: 8 residues processed: 156 average time/residue: 1.1112 time to fit residues: 189.5575 Evaluate side-chains 143 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN A 613 HIS B 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098121 restraints weight = 16409.833| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.29 r_work: 0.3177 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11722 Z= 0.095 Angle : 0.455 6.678 16144 Z= 0.234 Chirality : 0.037 0.153 1877 Planarity : 0.003 0.044 1862 Dihedral : 14.094 79.848 2249 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.35 % Allowed : 16.79 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1286 helix: 1.83 (0.20), residues: 664 sheet: -0.17 (0.49), residues: 105 loop : -0.48 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS C 36 PHE 0.017 0.001 PHE A 920 TYR 0.011 0.001 TYR A 788 ARG 0.006 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 627) hydrogen bonds : angle 3.46541 ( 1726) metal coordination : bond 0.00383 ( 8) metal coordination : angle 1.69637 ( 6) covalent geometry : bond 0.00206 (11714) covalent geometry : angle 0.45369 (16138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.133 Fit side-chains REVERT: A 284 ASP cc_start: 0.8561 (m-30) cc_final: 0.8281 (t0) REVERT: A 552 ASN cc_start: 0.8503 (p0) cc_final: 0.8294 (p0) REVERT: B 79 LYS cc_start: 0.6083 (mmtp) cc_final: 0.5406 (ptpt) REVERT: C 34 GLN cc_start: 0.8313 (tp40) cc_final: 0.8015 (tp40) REVERT: C 47 GLU cc_start: 0.8162 (mp0) cc_final: 0.7960 (mp0) outliers start: 26 outliers final: 13 residues processed: 156 average time/residue: 1.0559 time to fit residues: 181.2415 Evaluate side-chains 146 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 0.0020 chunk 125 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN A 613 HIS B 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093213 restraints weight = 16200.654| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.05 r_work: 0.3056 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 11722 Z= 0.303 Angle : 0.607 7.817 16144 Z= 0.313 Chirality : 0.043 0.174 1877 Planarity : 0.004 0.056 1862 Dihedral : 14.145 76.825 2249 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.43 % Allowed : 17.15 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 0.71 (0.23), residues: 1286 helix: 1.46 (0.20), residues: 676 sheet: -0.17 (0.51), residues: 97 loop : -0.70 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 916 HIS 0.009 0.001 HIS C 36 PHE 0.017 0.002 PHE A 652 TYR 0.032 0.002 TYR D 138 ARG 0.004 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 627) hydrogen bonds : angle 3.83207 ( 1726) metal coordination : bond 0.00914 ( 8) metal coordination : angle 1.85704 ( 6) covalent geometry : bond 0.00715 (11714) covalent geometry : angle 0.60629 (16138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 2.367 Fit side-chains REVERT: B 79 LYS cc_start: 0.6239 (mmtp) cc_final: 0.5390 (ptpt) REVERT: B 85 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7409 (p) REVERT: C 34 GLN cc_start: 0.8442 (tp40) cc_final: 0.8176 (tp40) REVERT: D 142 CYS cc_start: 0.6558 (m) cc_final: 0.6303 (m) outliers start: 38 outliers final: 16 residues processed: 156 average time/residue: 1.7343 time to fit residues: 295.2936 Evaluate side-chains 145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 170 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN B 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097942 restraints weight = 16504.261| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.03 r_work: 0.3116 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11722 Z= 0.108 Angle : 0.495 7.512 16144 Z= 0.255 Chirality : 0.038 0.181 1877 Planarity : 0.003 0.045 1862 Dihedral : 14.151 80.768 2249 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.35 % Allowed : 19.31 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1286 helix: 1.87 (0.20), residues: 668 sheet: -0.30 (0.48), residues: 105 loop : -0.36 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 PHE 0.018 0.001 PHE A 741 TYR 0.019 0.001 TYR D 138 ARG 0.006 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 627) hydrogen bonds : angle 3.57092 ( 1726) metal coordination : bond 0.00457 ( 8) metal coordination : angle 1.91027 ( 6) covalent geometry : bond 0.00238 (11714) covalent geometry : angle 0.49407 (16138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 2.014 Fit side-chains REVERT: A 552 ASN cc_start: 0.8954 (p0) cc_final: 0.8701 (p0) REVERT: B 79 LYS cc_start: 0.6105 (mmtp) cc_final: 0.5333 (ptpt) REVERT: B 85 SER cc_start: 0.7716 (t) cc_final: 0.7350 (p) REVERT: C 18 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8880 (tm-30) REVERT: C 34 GLN cc_start: 0.8391 (tp40) cc_final: 0.8116 (tp40) REVERT: D 138 TYR cc_start: 0.8823 (t80) cc_final: 0.8540 (t80) outliers start: 26 outliers final: 16 residues processed: 152 average time/residue: 1.7836 time to fit residues: 296.2971 Evaluate side-chains 149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 35 optimal weight: 0.0370 chunk 103 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.139122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093363 restraints weight = 16431.411| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.31 r_work: 0.3096 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11722 Z= 0.165 Angle : 0.523 9.391 16144 Z= 0.268 Chirality : 0.039 0.179 1877 Planarity : 0.003 0.048 1862 Dihedral : 14.118 80.488 2249 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.62 % Allowed : 19.31 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1286 helix: 1.72 (0.20), residues: 683 sheet: -0.26 (0.49), residues: 105 loop : -0.49 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.016 0.001 PHE A 741 TYR 0.018 0.001 TYR D 138 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 627) hydrogen bonds : angle 3.62431 ( 1726) metal coordination : bond 0.00537 ( 8) metal coordination : angle 1.57409 ( 6) covalent geometry : bond 0.00386 (11714) covalent geometry : angle 0.52174 (16138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.300 Fit side-chains REVERT: A 119 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6265 (tp) REVERT: A 899 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7225 (mmt) REVERT: B 79 LYS cc_start: 0.6167 (mmtp) cc_final: 0.5423 (ptpt) REVERT: C 18 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8912 (tm-30) REVERT: C 34 GLN cc_start: 0.8459 (tp40) cc_final: 0.8205 (tp40) outliers start: 29 outliers final: 21 residues processed: 150 average time/residue: 1.1452 time to fit residues: 187.3415 Evaluate side-chains 153 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 54 optimal weight: 0.0170 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.141617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098464 restraints weight = 16569.917| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.02 r_work: 0.3128 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11722 Z= 0.103 Angle : 0.498 9.403 16144 Z= 0.254 Chirality : 0.037 0.198 1877 Planarity : 0.003 0.044 1862 Dihedral : 14.133 81.991 2249 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.26 % Allowed : 19.86 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1286 helix: 1.93 (0.20), residues: 675 sheet: -0.23 (0.49), residues: 105 loop : -0.28 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 PHE 0.017 0.001 PHE A 741 TYR 0.014 0.001 TYR D 138 ARG 0.007 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 627) hydrogen bonds : angle 3.51135 ( 1726) metal coordination : bond 0.00377 ( 8) metal coordination : angle 1.52900 ( 6) covalent geometry : bond 0.00229 (11714) covalent geometry : angle 0.49719 (16138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.252 Fit side-chains REVERT: A 33 ARG cc_start: 0.7025 (mtm110) cc_final: 0.6818 (mtm110) REVERT: A 552 ASN cc_start: 0.8976 (p0) cc_final: 0.8754 (p0) REVERT: B 79 LYS cc_start: 0.6132 (mmtp) cc_final: 0.5350 (ptpt) REVERT: C 18 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8895 (tm-30) REVERT: C 34 GLN cc_start: 0.8395 (tp40) cc_final: 0.8117 (tp40) REVERT: D 138 TYR cc_start: 0.8857 (t80) cc_final: 0.8591 (t80) REVERT: D 142 CYS cc_start: 0.6409 (m) cc_final: 0.6178 (m) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 1.1161 time to fit residues: 186.7346 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.140114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098336 restraints weight = 16417.850| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.90 r_work: 0.3088 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11722 Z= 0.141 Angle : 0.527 11.601 16144 Z= 0.266 Chirality : 0.038 0.191 1877 Planarity : 0.003 0.047 1862 Dihedral : 14.108 81.355 2249 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.62 % Allowed : 19.86 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1286 helix: 1.89 (0.20), residues: 674 sheet: -0.18 (0.49), residues: 105 loop : -0.23 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 154 HIS 0.005 0.001 HIS C 36 PHE 0.017 0.001 PHE A 741 TYR 0.018 0.001 TYR D 138 ARG 0.007 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 627) hydrogen bonds : angle 3.57257 ( 1726) metal coordination : bond 0.00526 ( 8) metal coordination : angle 1.40407 ( 6) covalent geometry : bond 0.00328 (11714) covalent geometry : angle 0.52618 (16138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.538 Fit side-chains REVERT: A 899 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7176 (mmt) REVERT: B 79 LYS cc_start: 0.6142 (mmtp) cc_final: 0.5327 (ptpt) REVERT: C 18 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8901 (tm-30) REVERT: C 34 GLN cc_start: 0.8396 (tp40) cc_final: 0.8120 (tp40) REVERT: D 138 TYR cc_start: 0.8894 (t80) cc_final: 0.8643 (t80) outliers start: 29 outliers final: 18 residues processed: 150 average time/residue: 1.3584 time to fit residues: 222.9555 Evaluate side-chains 149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.141165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097773 restraints weight = 16380.119| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.12 r_work: 0.3114 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11722 Z= 0.113 Angle : 0.515 11.587 16144 Z= 0.260 Chirality : 0.037 0.159 1877 Planarity : 0.003 0.046 1862 Dihedral : 14.114 81.641 2249 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.17 % Allowed : 20.67 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1286 helix: 1.93 (0.20), residues: 674 sheet: -0.19 (0.48), residues: 105 loop : -0.18 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 PHE 0.017 0.001 PHE A 741 TYR 0.018 0.001 TYR D 138 ARG 0.007 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 627) hydrogen bonds : angle 3.54014 ( 1726) metal coordination : bond 0.00431 ( 8) metal coordination : angle 1.38830 ( 6) covalent geometry : bond 0.00257 (11714) covalent geometry : angle 0.51401 (16138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.121 Fit side-chains REVERT: A 33 ARG cc_start: 0.7028 (mtm110) cc_final: 0.6808 (mtm110) REVERT: A 260 ASP cc_start: 0.7986 (t0) cc_final: 0.7756 (t0) REVERT: A 899 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7151 (mmt) REVERT: C 18 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8924 (tm-30) REVERT: C 34 GLN cc_start: 0.8379 (tp40) cc_final: 0.8111 (tp40) outliers start: 24 outliers final: 19 residues processed: 150 average time/residue: 1.1255 time to fit residues: 185.3043 Evaluate side-chains 154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 121 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 127 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.139540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095602 restraints weight = 16270.937| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.04 r_work: 0.3091 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11722 Z= 0.158 Angle : 0.538 12.455 16144 Z= 0.274 Chirality : 0.039 0.173 1877 Planarity : 0.003 0.050 1862 Dihedral : 14.101 80.441 2249 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 20.76 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1286 helix: 1.84 (0.20), residues: 674 sheet: -0.23 (0.48), residues: 105 loop : -0.25 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.016 0.001 PHE A 741 TYR 0.022 0.002 TYR D 138 ARG 0.007 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 627) hydrogen bonds : angle 3.64808 ( 1726) metal coordination : bond 0.00543 ( 8) metal coordination : angle 1.41638 ( 6) covalent geometry : bond 0.00369 (11714) covalent geometry : angle 0.53781 (16138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10515.65 seconds wall clock time: 187 minutes 54.71 seconds (11274.71 seconds total)