Starting phenix.real_space_refine on Wed Mar 4 06:08:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yyt_11007/03_2026/6yyt_11007_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yyt_11007/03_2026/6yyt_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_11007/03_2026/6yyt_11007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yyt_11007/03_2026/6yyt_11007.map" model { file = "/net/cci-nas-00/data/ceres_data/6yyt_11007/03_2026/6yyt_11007_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yyt_11007/03_2026/6yyt_11007_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'PHE:plan': 2, 'TYR:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} 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: {'PHE:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} 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: 2.55, per 1000 atoms: 0.22 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: 0.74 Conformation dependent library (CDL) restraints added in 455.7 milliseconds 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: 1.27 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: 2.35 Time building geometry restraints manager: 0.98 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: 1.040 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.520 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- 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 : 2.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A 836 TYR 0.013 0.001 TYR A 788 PHE 0.010 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00259 (11714) covalent geometry : angle 0.47097 (16138) hydrogen bonds : bond 0.13011 ( 627) hydrogen bonds : angle 5.22944 ( 1726) metal coordination : bond 0.08428 ( 8) metal coordination : angle 16.70365 ( 6) *********************** 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 : 0.482 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: 0.4933 time to fit residues: 95.8523 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 : 0.377 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 B 88 GLN B 140 ASN D 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.140123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096347 restraints weight = 16346.883| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.96 r_work: 0.3101 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11722 Z= 0.232 Angle : 0.558 6.475 16144 Z= 0.288 Chirality : 0.041 0.171 1877 Planarity : 0.004 0.069 1862 Dihedral : 14.143 74.877 2251 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.71 % Allowed : 13.00 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.22), residues: 1286 helix: 1.06 (0.20), residues: 661 sheet: -0.65 (0.47), residues: 115 loop : -1.04 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 111 TYR 0.019 0.002 TYR B 135 PHE 0.021 0.002 PHE A 920 TRP 0.012 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00547 (11714) covalent geometry : angle 0.55584 (16138) hydrogen bonds : bond 0.04086 ( 627) hydrogen bonds : angle 3.82609 ( 1726) metal coordination : bond 0.01044 ( 8) metal coordination : angle 2.83200 ( 6) *********************** 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 176 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.365 Fit side-chains REVERT: A 33 ARG cc_start: 0.6985 (mtm110) cc_final: 0.6771 (mtm110) REVERT: A 119 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6256 (tp) REVERT: A 418 ASP cc_start: 0.8680 (m-30) cc_final: 0.8453 (t0) REVERT: A 722 ASN cc_start: 0.7912 (m110) cc_final: 0.7595 (m-40) REVERT: B 79 LYS cc_start: 0.6214 (mmtp) cc_final: 0.5406 (ptpt) REVERT: B 108 ASN cc_start: 0.6895 (m-40) cc_final: 0.6668 (m-40) REVERT: C 34 GLN cc_start: 0.8347 (tp40) cc_final: 0.8060 (tp40) REVERT: D 189 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8935 (mm) outliers start: 30 outliers final: 13 residues processed: 161 average time/residue: 0.5099 time to fit residues: 89.4942 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU 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 359 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 20 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.141542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.099265 restraints weight = 16479.117| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.85 r_work: 0.3142 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1972 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= 0.124 Angle : 0.477 6.079 16144 Z= 0.247 Chirality : 0.038 0.155 1877 Planarity : 0.003 0.052 1862 Dihedral : 14.146 75.735 2249 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.89 % Allowed : 15.52 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1286 helix: 1.52 (0.20), residues: 660 sheet: -0.40 (0.49), residues: 105 loop : -0.74 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 111 TYR 0.012 0.001 TYR A 289 PHE 0.020 0.001 PHE A 920 TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00281 (11714) covalent geometry : angle 0.47572 (16138) hydrogen bonds : bond 0.03305 ( 627) hydrogen bonds : angle 3.63476 ( 1726) metal coordination : bond 0.00467 ( 8) metal coordination : angle 2.14834 ( 6) *********************** 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 172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6918 (mtm110) cc_final: 0.6683 (mtm110) REVERT: A 260 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7497 (t0) REVERT: A 284 ASP cc_start: 0.8635 (t0) cc_final: 0.8257 (m-30) REVERT: A 418 ASP cc_start: 0.8632 (m-30) cc_final: 0.8407 (t0) REVERT: B 79 LYS cc_start: 0.6090 (mmtp) cc_final: 0.5352 (ptpt) REVERT: B 90 MET cc_start: 0.7573 (ttp) cc_final: 0.7365 (tmm) REVERT: C 34 GLN cc_start: 0.8346 (tp40) cc_final: 0.8084 (tp40) REVERT: D 67 MET cc_start: 0.5814 (tpt) cc_final: 0.4926 (ttm) outliers start: 32 outliers final: 9 residues processed: 156 average time/residue: 0.5038 time to fit residues: 85.8823 Evaluate side-chains 144 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 246 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 40.0000 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 85 optimal weight: 50.0000 chunk 72 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092637 restraints weight = 16484.407| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.34 r_work: 0.3050 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11722 Z= 0.273 Angle : 0.591 7.937 16144 Z= 0.305 Chirality : 0.043 0.173 1877 Planarity : 0.004 0.056 1862 Dihedral : 14.183 76.048 2249 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.25 % Allowed : 18.05 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1286 helix: 1.35 (0.20), residues: 674 sheet: -0.45 (0.48), residues: 107 loop : -0.82 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 57 TYR 0.020 0.002 TYR A 149 PHE 0.017 0.002 PHE A 652 TRP 0.014 0.001 TRP A 916 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00644 (11714) covalent geometry : angle 0.58991 (16138) hydrogen bonds : bond 0.04414 ( 627) hydrogen bonds : angle 3.85057 ( 1726) metal coordination : bond 0.00882 ( 8) metal coordination : angle 1.85388 ( 6) *********************** 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 171 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.413 Fit side-chains REVERT: A 119 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6291 (tp) REVERT: A 668 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.7657 (tmt) REVERT: A 899 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7270 (mmt) REVERT: B 79 LYS cc_start: 0.6326 (mmtp) cc_final: 0.5457 (ptpt) REVERT: C 34 GLN cc_start: 0.8506 (tp40) cc_final: 0.8257 (tp40) outliers start: 36 outliers final: 14 residues processed: 156 average time/residue: 0.5309 time to fit residues: 90.2512 Evaluate side-chains 146 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 668 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 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 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.141009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098649 restraints weight = 16333.647| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.85 r_work: 0.3132 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11722 Z= 0.108 Angle : 0.480 7.493 16144 Z= 0.247 Chirality : 0.038 0.182 1877 Planarity : 0.003 0.047 1862 Dihedral : 14.177 80.495 2249 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.16 % Allowed : 18.68 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1286 helix: 1.85 (0.20), residues: 665 sheet: -0.37 (0.48), residues: 105 loop : -0.52 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 111 TYR 0.013 0.001 TYR A 149 PHE 0.019 0.001 PHE A 920 TRP 0.013 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00240 (11714) covalent geometry : angle 0.47886 (16138) hydrogen bonds : bond 0.03137 ( 627) hydrogen bonds : angle 3.55616 ( 1726) metal coordination : bond 0.00446 ( 8) metal coordination : angle 1.95106 ( 6) *********************** 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 169 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.413 Fit side-chains REVERT: A 899 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7144 (mmt) REVERT: B 79 LYS cc_start: 0.6194 (mmtp) cc_final: 0.5446 (ptpt) REVERT: C 18 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8900 (tm-30) REVERT: C 34 GLN cc_start: 0.8407 (tp40) cc_final: 0.8156 (tp40) outliers start: 35 outliers final: 17 residues processed: 156 average time/residue: 0.5256 time to fit residues: 89.2688 Evaluate side-chains 148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 535 VAL Chi-restraints excluded: chain A residue 684 ASP 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 107 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR 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 Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.140426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096097 restraints weight = 16325.773| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.23 r_work: 0.3105 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11722 Z= 0.123 Angle : 0.492 7.910 16144 Z= 0.252 Chirality : 0.038 0.182 1877 Planarity : 0.003 0.046 1862 Dihedral : 14.132 81.293 2249 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.43 % Allowed : 18.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1286 helix: 1.95 (0.20), residues: 667 sheet: -0.30 (0.49), residues: 105 loop : -0.47 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.014 0.001 TYR A 217 PHE 0.016 0.001 PHE A 920 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00282 (11714) covalent geometry : angle 0.49123 (16138) hydrogen bonds : bond 0.03225 ( 627) hydrogen bonds : angle 3.52963 ( 1726) metal coordination : bond 0.00455 ( 8) metal coordination : angle 1.50015 ( 6) *********************** 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 170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.307 Fit side-chains REVERT: A 119 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6170 (tp) REVERT: A 260 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7739 (t0) REVERT: A 899 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6987 (mmt) REVERT: B 79 LYS cc_start: 0.6098 (mmtp) cc_final: 0.5340 (ptpt) REVERT: C 18 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8872 (tm-30) REVERT: C 34 GLN cc_start: 0.8400 (tp40) cc_final: 0.8114 (tp40) REVERT: D 164 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8585 (p) outliers start: 38 outliers final: 21 residues processed: 154 average time/residue: 0.5326 time to fit residues: 89.2471 Evaluate side-chains 154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 260 ASP 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 573 GLN 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 173 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR 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 Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.138187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094748 restraints weight = 16449.841| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.92 r_work: 0.3070 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11722 Z= 0.209 Angle : 0.539 7.922 16144 Z= 0.280 Chirality : 0.040 0.187 1877 Planarity : 0.003 0.052 1862 Dihedral : 14.137 80.067 2249 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.43 % Allowed : 19.31 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.23), residues: 1286 helix: 1.72 (0.20), residues: 678 sheet: -0.16 (0.51), residues: 97 loop : -0.64 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 111 TYR 0.016 0.002 TYR A 149 PHE 0.015 0.002 PHE A 440 TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00493 (11714) covalent geometry : angle 0.53813 (16138) hydrogen bonds : bond 0.03815 ( 627) hydrogen bonds : angle 3.65431 ( 1726) metal coordination : bond 0.00646 ( 8) metal coordination : angle 1.54312 ( 6) *********************** 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 170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.420 Fit side-chains REVERT: A 119 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6265 (tp) REVERT: A 899 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7119 (mmt) REVERT: A 924 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8551 (mmm) REVERT: B 79 LYS cc_start: 0.6204 (mmtp) cc_final: 0.5427 (ptpt) REVERT: C 18 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8917 (tm-30) REVERT: C 34 GLN cc_start: 0.8460 (tp40) cc_final: 0.8193 (tp40) REVERT: D 164 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8667 (p) outliers start: 38 outliers final: 23 residues processed: 154 average time/residue: 0.5318 time to fit residues: 89.2173 Evaluate side-chains 158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 424 VAL 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 A residue 924 MET 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 B residue 187 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 164 SER 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 17 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.140404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.096972 restraints weight = 16349.948| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.06 r_work: 0.3114 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11722 Z= 0.120 Angle : 0.511 9.800 16144 Z= 0.262 Chirality : 0.038 0.188 1877 Planarity : 0.003 0.047 1862 Dihedral : 14.143 81.682 2249 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.80 % Allowed : 20.31 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.23), residues: 1286 helix: 1.88 (0.20), residues: 673 sheet: -0.31 (0.49), residues: 105 loop : -0.33 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 111 TYR 0.013 0.001 TYR A 217 PHE 0.017 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00270 (11714) covalent geometry : angle 0.51070 (16138) hydrogen bonds : bond 0.03198 ( 627) hydrogen bonds : angle 3.56550 ( 1726) metal coordination : bond 0.00468 ( 8) metal coordination : angle 1.55951 ( 6) *********************** 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 163 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.407 Fit side-chains REVERT: A 899 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.7017 (mmt) REVERT: B 79 LYS cc_start: 0.6116 (mmtp) cc_final: 0.5358 (ptpt) REVERT: B 85 SER cc_start: 0.7735 (t) cc_final: 0.7368 (p) REVERT: C 18 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8893 (tm-30) REVERT: C 34 GLN cc_start: 0.8391 (tp40) cc_final: 0.8105 (tp40) REVERT: D 164 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8643 (p) outliers start: 31 outliers final: 24 residues processed: 152 average time/residue: 0.5168 time to fit residues: 85.7693 Evaluate side-chains 156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 394 THR 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 899 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR 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 90 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.139264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.097144 restraints weight = 16285.048| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.87 r_work: 0.3078 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2763 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= 0.161 Angle : 0.537 12.250 16144 Z= 0.273 Chirality : 0.039 0.197 1877 Planarity : 0.003 0.051 1862 Dihedral : 14.127 81.166 2249 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.07 % Allowed : 20.58 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1286 helix: 1.80 (0.20), residues: 672 sheet: -0.32 (0.49), residues: 105 loop : -0.36 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 111 TYR 0.015 0.001 TYR B 135 PHE 0.016 0.001 PHE A 440 TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00378 (11714) covalent geometry : angle 0.53625 (16138) hydrogen bonds : bond 0.03485 ( 627) hydrogen bonds : angle 3.62246 ( 1726) metal coordination : bond 0.00546 ( 8) metal coordination : angle 1.48480 ( 6) *********************** 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 164 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.406 Fit side-chains REVERT: A 899 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.7053 (mmt) REVERT: A 924 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8512 (mmm) REVERT: B 79 LYS cc_start: 0.6129 (mmtp) cc_final: 0.5353 (ptpt) REVERT: C 18 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8902 (tm-30) REVERT: C 34 GLN cc_start: 0.8396 (tp40) cc_final: 0.8106 (tp40) REVERT: D 164 SER cc_start: 0.8893 (m) cc_final: 0.8652 (p) outliers start: 34 outliers final: 23 residues processed: 151 average time/residue: 0.5420 time to fit residues: 89.0738 Evaluate side-chains 155 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 394 THR 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 899 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR 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 90 MET 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 77 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 53 optimal weight: 0.3980 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.140600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098596 restraints weight = 16490.566| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.90 r_work: 0.3100 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2755 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= 0.119 Angle : 0.519 11.718 16144 Z= 0.263 Chirality : 0.038 0.192 1877 Planarity : 0.003 0.047 1862 Dihedral : 14.129 81.662 2249 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.62 % Allowed : 21.30 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1286 helix: 1.86 (0.20), residues: 673 sheet: -0.30 (0.48), residues: 105 loop : -0.26 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 111 TYR 0.013 0.001 TYR B 135 PHE 0.016 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00272 (11714) covalent geometry : angle 0.51836 (16138) hydrogen bonds : bond 0.03174 ( 627) hydrogen bonds : angle 3.57802 ( 1726) metal coordination : bond 0.00452 ( 8) metal coordination : angle 1.42431 ( 6) ********************** 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 162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.390 Fit side-chains REVERT: A 758 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 899 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.7021 (mmt) REVERT: B 79 LYS cc_start: 0.6131 (mmtp) cc_final: 0.5319 (ptpt) REVERT: C 18 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8912 (tm-30) REVERT: C 34 GLN cc_start: 0.8371 (tp40) cc_final: 0.8086 (tp40) REVERT: D 111 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8762 (ttp-110) REVERT: D 164 SER cc_start: 0.8902 (m) cc_final: 0.8642 (p) outliers start: 29 outliers final: 24 residues processed: 153 average time/residue: 0.5403 time to fit residues: 89.9463 Evaluate side-chains 157 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 394 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 573 GLN 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 758 LEU 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 173 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 124 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094878 restraints weight = 16434.301| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.97 r_work: 0.3051 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11722 Z= 0.247 Angle : 0.595 12.644 16144 Z= 0.304 Chirality : 0.042 0.172 1877 Planarity : 0.004 0.056 1862 Dihedral : 14.125 79.495 2249 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.16 % Allowed : 20.94 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1286 helix: 1.44 (0.20), residues: 687 sheet: -0.22 (0.50), residues: 97 loop : -0.54 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.038 0.002 TYR D 138 PHE 0.016 0.002 PHE A 741 TRP 0.014 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00585 (11714) covalent geometry : angle 0.59476 (16138) hydrogen bonds : bond 0.04063 ( 627) hydrogen bonds : angle 3.82251 ( 1726) metal coordination : bond 0.00756 ( 8) metal coordination : angle 1.46434 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4457.65 seconds wall clock time: 76 minutes 30.30 seconds (4590.30 seconds total)