Starting phenix.real_space_refine on Sat Oct 11 12:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkp_41356/10_2025/8tkp_41356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkp_41356/10_2025/8tkp_41356.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/8tkp_41356/10_2025/8tkp_41356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkp_41356/10_2025/8tkp_41356.map" model { file = "/net/cci-nas-00/data/ceres_data/8tkp_41356/10_2025/8tkp_41356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkp_41356/10_2025/8tkp_41356.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= 0.001 sd= 0.009 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 Ca 4 9.91 5 P 10 5.49 5 S 74 5.16 5 C 9731 2.51 5 N 2347 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14666 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4992 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 378 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 4992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4992 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 378 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 291 Unusual residues: {'CLR': 1, 'NAG': 1, 'PEE': 4, 'R16': 9, 'TWT': 2} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 82 Unusual residues: {'PEE': 1, 'PLM': 2, 'R16': 2, 'TWT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'PLM:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 320 Unusual residues: {'CLR': 1, 'NAG': 1, 'PEE': 5, 'R16': 9, 'TWT': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'PLM': 2, 'R16': 2, 'TWT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PLM:plan-1': 2} Unresolved non-hydrogen planarities: 2 Residues with excluded nonbonded symmetry interactions: 134 residue: pdb=" N LYS A 95 " occ=0.97 ... (7 atoms not shown) pdb=" NZ LYS A 95 " occ=0.94 residue: pdb=" N GLU A 102 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU A 102 " occ=0.56 residue: pdb=" N LYS A 106 " occ=0.95 ... (7 atoms not shown) pdb=" NZ LYS A 106 " occ=0.72 residue: pdb=" N GLU A 132 " occ=0.94 ... (7 atoms not shown) pdb=" OE2 GLU A 132 " occ=0.87 residue: pdb=" N ALA A 133 " occ=0.95 ... (3 atoms not shown) pdb=" CB ALA A 133 " occ=0.91 residue: pdb=" N GLY A 146 " occ=0.93 ... (2 atoms not shown) pdb=" O GLY A 146 " occ=0.91 residue: pdb=" N LEU A 149 " occ=0.89 ... (6 atoms not shown) pdb=" CD2 LEU A 149 " occ=0.93 residue: pdb=" N ASP A 157 " occ=0.91 ... (6 atoms not shown) pdb=" OD2 ASP A 157 " occ=0.83 residue: pdb=" N ASN A 158 " occ=0.78 ... (6 atoms not shown) pdb=" ND2 ASN A 158 " occ=0.85 residue: pdb=" N ASP A 214 " occ=0.98 ... (6 atoms not shown) pdb=" OD2 ASP A 214 " occ=0.69 residue: pdb=" N GLY A 251 " occ=0.98 ... (2 atoms not shown) pdb=" O GLY A 251 " occ=0.89 residue: pdb=" N THR A 268 " occ=0.99 ... (5 atoms not shown) pdb=" CG2 THR A 268 " occ=0.94 ... (remaining 122 not shown) Time building chain proxies: 3.57, per 1000 atoms: 0.24 Number of scatterers: 14666 At special positions: 0 Unit cell: (139.608, 111.354, 112.185, 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) Ca 4 19.99 S 74 16.00 P 10 15.00 O 2500 8.00 N 2347 7.00 C 9731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 594 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS D 594 " - pdb=" SG CYS D 743 " distance=2.03 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=5, symmetry=0 Links applied BETA1-3 " NAG H 1 " - " NAG H 2 " BETA1-4 " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1316 " - " ASN A 748 " " NAG D1316 " - " ASN D 748 " " NAG G 1 " - " ASN A 225 " " NAG H 1 " - " ASN D 225 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 632.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 4 sheets defined 76.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 89 through 107 removed outlier: 4.388A pdb=" N ILE A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 113 through 131 Processing helix chain 'A' and resid 136 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 178 through 206 removed outlier: 3.945A pdb=" N TYR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 221 through 232 removed outlier: 5.426A pdb=" N ALA A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.661A pdb=" N PHE A 263 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 308 removed outlier: 4.132A pdb=" N GLY A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 312 removed outlier: 3.572A pdb=" N SER A 312 " --> pdb=" O THR A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 334 through 355 Processing helix chain 'A' and resid 366 through 395 Processing helix chain 'A' and resid 405 through 430 Proline residue: A 419 - end of helix removed outlier: 3.531A pdb=" N LYS A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 471 removed outlier: 3.750A pdb=" N LYS A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.765A pdb=" N GLN A 590 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 622 Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 651 through 670 Processing helix chain 'A' and resid 675 through 698 removed outlier: 3.596A pdb=" N CYS A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 737 removed outlier: 3.694A pdb=" N LEU A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Proline residue: A 729 - end of helix Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 767 through 776 Processing helix chain 'A' and resid 777 through 813 removed outlier: 3.820A pdb=" N ILE A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Proline residue: A 783 - end of helix removed outlier: 3.515A pdb=" N PHE A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.738A pdb=" N ASN B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.411A pdb=" N GLU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 155 through 171 Processing helix chain 'B' and resid 179 through 189 removed outlier: 4.203A pdb=" N ARG B 189 " --> pdb=" O HIS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'C' and resid 24 through 47 removed outlier: 3.648A pdb=" N PHE C 45 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 59 through 62 Processing helix chain 'D' and resid 89 through 89 No H-bonds generated for 'chain 'D' and resid 89 through 89' Processing helix chain 'D' and resid 90 through 107 removed outlier: 3.859A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 113 through 131 Processing helix chain 'D' and resid 137 through 161 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 178 through 206 removed outlier: 3.847A pdb=" N TYR D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 221 through 232 removed outlier: 5.213A pdb=" N ALA D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 277 through 306 Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'D' and resid 334 through 355 Processing helix chain 'D' and resid 367 through 396 Processing helix chain 'D' and resid 405 through 429 Proline residue: D 419 - end of helix Processing helix chain 'D' and resid 432 through 470 Processing helix chain 'D' and resid 584 through 588 Processing helix chain 'D' and resid 594 through 622 Processing helix chain 'D' and resid 622 through 632 Processing helix chain 'D' and resid 651 through 670 Processing helix chain 'D' and resid 675 through 698 Processing helix chain 'D' and resid 713 through 737 Proline residue: D 729 - end of helix Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 765 through 776 removed outlier: 3.509A pdb=" N VAL D 769 " --> pdb=" O ASP D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 813 removed outlier: 3.972A pdb=" N ILE D 781 " --> pdb=" O SER D 777 " (cutoff:3.500A) Proline residue: D 783 - end of helix Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 35 through 50 removed outlier: 3.706A pdb=" N ASN E 50 " --> pdb=" O PHE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 76 through 81 removed outlier: 4.342A pdb=" N GLU E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 93 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 117 through 130 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 155 through 169 Processing helix chain 'E' and resid 179 through 188 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'F' and resid 23 through 47 removed outlier: 3.566A pdb=" N ARG F 47 " --> pdb=" O CYS F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 60 removed outlier: 3.668A pdb=" N ILE F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'E' and resid 67 through 69 924 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2170 1.30 - 1.43: 3945 1.43 - 1.55: 8703 1.55 - 1.68: 20 1.68 - 1.81: 122 Bond restraints: 14960 Sorted by residual: bond pdb=" CA SER A 775 " pdb=" C SER A 775 " ideal model delta sigma weight residual 1.524 1.452 0.072 1.26e-02 6.30e+03 3.26e+01 bond pdb=" C ASN A 770 " pdb=" O ASN A 770 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.92e+01 bond pdb=" N LYS A 766 " pdb=" CA LYS A 766 " ideal model delta sigma weight residual 1.456 1.405 0.051 1.23e-02 6.61e+03 1.75e+01 bond pdb=" CA LYS A 766 " pdb=" C LYS A 766 " ideal model delta sigma weight residual 1.524 1.473 0.050 1.26e-02 6.30e+03 1.59e+01 bond pdb=" N GLN A 807 " pdb=" CA GLN A 807 " ideal model delta sigma weight residual 1.459 1.414 0.044 1.16e-02 7.43e+03 1.47e+01 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 19793 3.35 - 6.71: 187 6.71 - 10.06: 38 10.06 - 13.42: 2 13.42 - 16.77: 10 Bond angle restraints: 20030 Sorted by residual: angle pdb=" N TYR A 774 " pdb=" CA TYR A 774 " pdb=" C TYR A 774 " ideal model delta sigma weight residual 111.28 104.44 6.84 1.09e+00 8.42e-01 3.93e+01 angle pdb=" C VAL A 769 " pdb=" CA VAL A 769 " pdb=" CB VAL A 769 " ideal model delta sigma weight residual 112.14 104.18 7.96 1.35e+00 5.49e-01 3.47e+01 angle pdb=" N GLN A 807 " pdb=" CA GLN A 807 " pdb=" C GLN A 807 " ideal model delta sigma weight residual 111.02 104.02 7.00 1.22e+00 6.72e-01 3.29e+01 angle pdb=" O3P PEE A1311 " pdb=" P PEE A1311 " pdb=" O4P PEE A1311 " ideal model delta sigma weight residual 92.91 109.68 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O3P PEE A1302 " pdb=" P PEE A1302 " pdb=" O4P PEE A1302 " ideal model delta sigma weight residual 92.91 109.62 -16.71 3.00e+00 1.11e-01 3.10e+01 ... (remaining 20025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 8961 35.57 - 71.14: 191 71.14 - 106.71: 43 106.71 - 142.29: 13 142.29 - 177.86: 10 Dihedral angle restraints: 9218 sinusoidal: 4242 harmonic: 4976 Sorted by residual: dihedral pdb=" C ASN A 763 " pdb=" N ASN A 763 " pdb=" CA ASN A 763 " pdb=" CB ASN A 763 " ideal model delta harmonic sigma weight residual -122.60 -138.81 16.21 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" N ASN A 763 " pdb=" C ASN A 763 " pdb=" CA ASN A 763 " pdb=" CB ASN A 763 " ideal model delta harmonic sigma weight residual 122.80 136.16 -13.36 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" C TYR A 774 " pdb=" N TYR A 774 " pdb=" CA TYR A 774 " pdb=" CB TYR A 774 " ideal model delta harmonic sigma weight residual -122.60 -110.09 -12.51 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 9215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2167 0.158 - 0.316: 16 0.316 - 0.473: 4 0.473 - 0.631: 0 0.631 - 0.789: 1 Chirality restraints: 2188 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O3 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.10e+01 chirality pdb=" CA ASN A 763 " pdb=" N ASN A 763 " pdb=" C ASN A 763 " pdb=" CB ASN A 763 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CA VAL A 799 " pdb=" N VAL A 799 " pdb=" C VAL A 799 " pdb=" CB VAL A 799 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 2185 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1316 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A1316 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A1316 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG A1316 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1316 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.306 2.00e-02 2.50e+03 2.59e-01 8.37e+02 pdb=" C7 NAG H 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.259 2.00e-02 2.50e+03 2.19e-01 5.97e+02 pdb=" C7 NAG G 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.370 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.005 2.00e-02 2.50e+03 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 8 1.90 - 2.65: 245 2.65 - 3.40: 20861 3.40 - 4.15: 33853 4.15 - 4.90: 63441 Nonbonded interactions: 118408 Sorted by model distance: nonbonded pdb=" CA GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.152 3.470 nonbonded pdb=" CA GLN A 804 " pdb=" CD GLN A 807 " model vdw 1.243 3.700 nonbonded pdb=" C GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.305 3.270 nonbonded pdb=" CD1 LEU A 809 " pdb=" CD2 LEU D 809 " model vdw 1.586 3.880 nonbonded pdb=" O GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.603 3.040 ... (remaining 118403 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 'A' and (resid 89 through 1305 or (resid 1307 and (name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 40 or name C41)) or (resid 1308 and (name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name C37)) or resid 1309 through 1316)) selection = (chain 'D' and (resid 89 through 813 or (resid 1301 and (name C1 or name C10 or \ name C11 or name C12 or name C2 or name C3 or name C4 or name C5 or name C6 or n \ ame C7 or name C8 or name C9 )) or resid 1302 through 1305 or (resid 1307 and (n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41)) or (resid 1308 and (name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37)) or (resid 1309 and \ (name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C40 or name C41 or name C42)) or (resid 1310 and (name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C40 or name C41 or name C42)) or resid 1311 through 1316)) } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 15 through 204) selection = (chain 'F' and (resid 15 through 62 or (resid 201 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or \ name C8 or name C9 )) or (resid 202 and (name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41)) or (resid 203 and (name C31 or name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 204 and (name CA or name C1 or name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O2 )))) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.16 max=1.00 mean=0.95 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: 8.350 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.200 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:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 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 : 0.005 0.074 14973 Z= 0.285 Angle : 0.915 16.771 20052 Z= 0.413 Chirality : 0.048 0.789 2188 Planarity : 0.011 0.295 2418 Dihedral : 16.841 177.858 5992 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.94 % Allowed : 6.89 % Favored : 92.17 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 2.30 (0.21), residues: 1682 helix: 2.40 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 195 TYR 0.037 0.001 TYR A 774 PHE 0.015 0.001 PHE E 105 TRP 0.008 0.001 TRP D 693 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00491 (14960) covalent geometry : angle 0.90850 (20030) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.01510 ( 4) hydrogen bonds : bond 0.11369 ( 924) hydrogen bonds : angle 5.06909 ( 2748) Misc. bond : bond 0.00090 ( 5) link_BETA1-3 : bond 0.00544 ( 1) link_BETA1-3 : angle 0.27173 ( 3) link_BETA1-4 : bond 0.00701 ( 1) link_BETA1-4 : angle 3.02954 ( 3) link_NAG-ASN : bond 0.00654 ( 4) link_NAG-ASN : angle 4.21578 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.1542 (mtm) cc_final: 0.1256 (mmm) REVERT: A 807 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6083 (mt0) REVERT: B 115 MET cc_start: 0.3999 (mmm) cc_final: 0.3544 (pmm) REVERT: C 26 MET cc_start: 0.1734 (mtp) cc_final: 0.1530 (ttm) REVERT: C 53 THR cc_start: 0.6565 (p) cc_final: 0.6220 (t) REVERT: D 157 ASP cc_start: 0.8944 (m-30) cc_final: 0.8485 (m-30) REVERT: D 292 PHE cc_start: 0.9182 (t80) cc_final: 0.8944 (t80) REVERT: D 437 LEU cc_start: 0.9460 (tp) cc_final: 0.9238 (tm) REVERT: D 710 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7554 (pmm150) REVERT: F 54 LYS cc_start: 0.9202 (tptt) cc_final: 0.8781 (tptt) outliers start: 14 outliers final: 3 residues processed: 253 average time/residue: 0.5449 time to fit residues: 153.3958 Evaluate side-chains 139 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain E residue 95 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 655 ASN A 763 ASN B 50 ASN D 110 GLN D 358 GLN D 590 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.157275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.092313 restraints weight = 44381.775| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 5.17 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 133 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14973 Z= 0.135 Angle : 0.661 10.819 20052 Z= 0.316 Chirality : 0.041 0.336 2188 Planarity : 0.004 0.043 2418 Dihedral : 17.195 175.959 2652 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.34 % Allowed : 14.06 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 2.25 (0.21), residues: 1682 helix: 2.31 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -0.68 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 238 TYR 0.029 0.001 TYR A 774 PHE 0.025 0.001 PHE A 732 TRP 0.014 0.001 TRP C 25 HIS 0.009 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00277 (14960) covalent geometry : angle 0.65090 (20030) SS BOND : bond 0.01730 ( 2) SS BOND : angle 1.54807 ( 4) hydrogen bonds : bond 0.04659 ( 924) hydrogen bonds : angle 4.22283 ( 2748) Misc. bond : bond 0.00055 ( 5) link_BETA1-3 : bond 0.00271 ( 1) link_BETA1-3 : angle 1.48158 ( 3) link_BETA1-4 : bond 0.00322 ( 1) link_BETA1-4 : angle 2.83716 ( 3) link_NAG-ASN : bond 0.00543 ( 4) link_NAG-ASN : angle 4.39388 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.4159 (mtm) cc_final: 0.3874 (mmm) REVERT: B 58 MET cc_start: 0.0020 (mmm) cc_final: -0.0617 (mpp) REVERT: B 115 MET cc_start: 0.3905 (mmm) cc_final: 0.3408 (pmm) REVERT: B 172 LEU cc_start: 0.3161 (OUTLIER) cc_final: 0.2819 (mt) REVERT: D 157 ASP cc_start: 0.9274 (m-30) cc_final: 0.9020 (m-30) REVERT: D 284 PHE cc_start: 0.9316 (m-80) cc_final: 0.8761 (m-80) REVERT: D 395 THR cc_start: 0.9263 (p) cc_final: 0.9063 (t) REVERT: D 588 MET cc_start: 0.8072 (mmm) cc_final: 0.7569 (mmm) REVERT: D 710 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7295 (pmm150) REVERT: E 107 ASP cc_start: 0.9319 (m-30) cc_final: 0.9082 (m-30) REVERT: F 54 LYS cc_start: 0.9387 (tptt) cc_final: 0.9095 (tptp) outliers start: 35 outliers final: 7 residues processed: 174 average time/residue: 0.4783 time to fit residues: 94.1033 Evaluate side-chains 132 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 36 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 140 optimal weight: 30.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.144986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.074640 restraints weight = 44945.938| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 4.97 r_work: 0.2999 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 133 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 159 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14973 Z= 0.145 Angle : 0.638 14.447 20052 Z= 0.303 Chirality : 0.042 0.338 2188 Planarity : 0.004 0.042 2418 Dihedral : 15.650 178.514 2647 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.08 % Allowed : 13.59 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 2.09 (0.21), residues: 1682 helix: 2.18 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 97 TYR 0.027 0.001 TYR D 261 PHE 0.026 0.001 PHE D 200 TRP 0.022 0.001 TRP C 25 HIS 0.007 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00317 (14960) covalent geometry : angle 0.63008 (20030) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.83780 ( 4) hydrogen bonds : bond 0.04250 ( 924) hydrogen bonds : angle 4.13237 ( 2748) Misc. bond : bond 0.00080 ( 5) link_BETA1-3 : bond 0.00011 ( 1) link_BETA1-3 : angle 1.31500 ( 3) link_BETA1-4 : bond 0.01008 ( 1) link_BETA1-4 : angle 2.75714 ( 3) link_NAG-ASN : bond 0.00402 ( 4) link_NAG-ASN : angle 3.95484 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: -0.0083 (OUTLIER) cc_final: -0.0579 (mmt) REVERT: A 190 TRP cc_start: 0.8826 (OUTLIER) cc_final: 0.8155 (t-100) REVERT: A 382 MET cc_start: 0.3933 (mtm) cc_final: 0.3709 (mmm) REVERT: B 115 MET cc_start: 0.3806 (mmm) cc_final: 0.3379 (pmm) REVERT: B 172 LEU cc_start: 0.3444 (OUTLIER) cc_final: 0.3173 (mt) REVERT: C 46 MET cc_start: 0.5785 (ptt) cc_final: 0.4903 (pp-130) REVERT: D 292 PHE cc_start: 0.9596 (t80) cc_final: 0.9385 (t80) REVERT: D 343 MET cc_start: 0.8985 (mpp) cc_final: 0.8652 (mpp) REVERT: D 439 PHE cc_start: 0.9689 (OUTLIER) cc_final: 0.9323 (m-80) REVERT: D 622 ASP cc_start: 0.9475 (m-30) cc_final: 0.9213 (m-30) REVERT: D 710 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7032 (pmm150) REVERT: D 774 TYR cc_start: 0.7059 (m-10) cc_final: 0.6780 (m-80) REVERT: F 54 LYS cc_start: 0.9466 (tptt) cc_final: 0.9208 (tptp) outliers start: 46 outliers final: 12 residues processed: 167 average time/residue: 0.4934 time to fit residues: 93.1912 Evaluate side-chains 142 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 665 MET Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 0 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 chunk 109 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 40.0000 chunk 69 optimal weight: 50.0000 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.139649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.069750 restraints weight = 45125.654| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.54 r_work: 0.2918 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 159 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 190 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 14973 Z= 0.309 Angle : 0.732 11.158 20052 Z= 0.355 Chirality : 0.045 0.319 2188 Planarity : 0.004 0.048 2418 Dihedral : 15.297 171.528 2647 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.21 % Allowed : 14.73 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.67 (0.21), residues: 1682 helix: 1.86 (0.15), residues: 1205 sheet: None (None), residues: 0 loop : -0.84 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 625 TYR 0.043 0.002 TYR D 261 PHE 0.022 0.002 PHE E 92 TRP 0.024 0.002 TRP C 25 HIS 0.008 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00696 (14960) covalent geometry : angle 0.72345 (20030) SS BOND : bond 0.00505 ( 2) SS BOND : angle 0.79365 ( 4) hydrogen bonds : bond 0.04573 ( 924) hydrogen bonds : angle 4.38582 ( 2748) Misc. bond : bond 0.00121 ( 5) link_BETA1-3 : bond 0.00343 ( 1) link_BETA1-3 : angle 2.21846 ( 3) link_BETA1-4 : bond 0.00452 ( 1) link_BETA1-4 : angle 2.97293 ( 3) link_NAG-ASN : bond 0.00887 ( 4) link_NAG-ASN : angle 4.13806 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: -0.0182 (OUTLIER) cc_final: -0.0708 (mmt) REVERT: A 382 MET cc_start: 0.3785 (mtm) cc_final: 0.3575 (mmm) REVERT: B 58 MET cc_start: -0.0114 (mpp) cc_final: -0.1146 (mtp) REVERT: B 115 MET cc_start: 0.3764 (mmm) cc_final: 0.3312 (pmm) REVERT: B 172 LEU cc_start: 0.3385 (OUTLIER) cc_final: 0.3138 (mt) REVERT: C 46 MET cc_start: 0.5806 (ptt) cc_final: 0.4656 (pp-130) REVERT: D 195 ASN cc_start: 0.9622 (OUTLIER) cc_final: 0.9126 (t0) REVERT: D 268 THR cc_start: 0.8980 (p) cc_final: 0.8719 (p) REVERT: D 270 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8692 (m-10) REVERT: D 343 MET cc_start: 0.9029 (mpp) cc_final: 0.8706 (mpp) REVERT: D 588 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7448 (mmm) REVERT: D 622 ASP cc_start: 0.9476 (m-30) cc_final: 0.9079 (m-30) REVERT: D 710 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7202 (pmm150) REVERT: F 47 ARG cc_start: 0.8856 (mmt90) cc_final: 0.8648 (mmt180) outliers start: 48 outliers final: 14 residues processed: 162 average time/residue: 0.5206 time to fit residues: 94.8357 Evaluate side-chains 136 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 588 MET Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 31 optimal weight: 0.0870 chunk 156 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 50.0000 chunk 144 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 655 ASN E 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.140680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072971 restraints weight = 44496.704| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.55 r_work: 0.2975 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 190 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 225 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14973 Z= 0.125 Angle : 0.653 13.196 20052 Z= 0.306 Chirality : 0.041 0.306 2188 Planarity : 0.004 0.042 2418 Dihedral : 14.557 175.801 2647 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.48 % Allowed : 16.47 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.85 (0.21), residues: 1682 helix: 1.99 (0.15), residues: 1203 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 62 TYR 0.016 0.001 TYR D 261 PHE 0.018 0.001 PHE A 283 TRP 0.038 0.001 TRP A 190 HIS 0.003 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00263 (14960) covalent geometry : angle 0.64543 (20030) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.60566 ( 4) hydrogen bonds : bond 0.04088 ( 924) hydrogen bonds : angle 4.14003 ( 2748) Misc. bond : bond 0.00079 ( 5) link_BETA1-3 : bond 0.00501 ( 1) link_BETA1-3 : angle 1.02851 ( 3) link_BETA1-4 : bond 0.00715 ( 1) link_BETA1-4 : angle 2.64689 ( 3) link_NAG-ASN : bond 0.00401 ( 4) link_NAG-ASN : angle 3.84208 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.3852 (mtm) cc_final: 0.3633 (mmm) REVERT: B 115 MET cc_start: 0.3804 (mmm) cc_final: 0.3346 (pmm) REVERT: B 172 LEU cc_start: 0.3309 (OUTLIER) cc_final: 0.3040 (mt) REVERT: C 46 MET cc_start: 0.5792 (ptt) cc_final: 0.4568 (pp-130) REVERT: D 195 ASN cc_start: 0.9616 (OUTLIER) cc_final: 0.9029 (t0) REVERT: D 268 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8516 (p) REVERT: D 304 ASN cc_start: 0.9500 (t0) cc_final: 0.9293 (t0) REVERT: D 343 MET cc_start: 0.9104 (mpp) cc_final: 0.8757 (mmt) REVERT: D 588 MET cc_start: 0.7732 (mmm) cc_final: 0.7379 (mmm) REVERT: D 622 ASP cc_start: 0.9460 (m-30) cc_final: 0.9039 (m-30) REVERT: D 710 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.6981 (pmm150) outliers start: 37 outliers final: 15 residues processed: 161 average time/residue: 0.4605 time to fit residues: 84.2983 Evaluate side-chains 144 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 123 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 87 optimal weight: 0.3980 chunk 13 optimal weight: 50.0000 chunk 55 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 ASN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.138611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.070343 restraints weight = 45077.240| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.21 r_work: 0.2941 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 225 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 266 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14973 Z= 0.193 Angle : 0.678 15.094 20052 Z= 0.322 Chirality : 0.043 0.322 2188 Planarity : 0.004 0.043 2418 Dihedral : 14.095 175.290 2647 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.74 % Allowed : 16.67 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.83 (0.21), residues: 1682 helix: 1.98 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 55 TYR 0.029 0.001 TYR D 261 PHE 0.018 0.001 PHE E 109 TRP 0.032 0.001 TRP C 25 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00435 (14960) covalent geometry : angle 0.67134 (20030) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.50597 ( 4) hydrogen bonds : bond 0.04158 ( 924) hydrogen bonds : angle 4.22603 ( 2748) Misc. bond : bond 0.00091 ( 5) link_BETA1-3 : bond 0.00049 ( 1) link_BETA1-3 : angle 1.55948 ( 3) link_BETA1-4 : bond 0.00864 ( 1) link_BETA1-4 : angle 2.65518 ( 3) link_NAG-ASN : bond 0.00354 ( 4) link_NAG-ASN : angle 3.78416 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: -0.0324 (OUTLIER) cc_final: -0.0885 (mmt) REVERT: A 382 MET cc_start: 0.3879 (mtm) cc_final: 0.3650 (mmm) REVERT: B 115 MET cc_start: 0.3811 (mmm) cc_final: 0.3324 (pmm) REVERT: B 172 LEU cc_start: 0.3307 (OUTLIER) cc_final: 0.3041 (mt) REVERT: C 46 MET cc_start: 0.5897 (ptt) cc_final: 0.4558 (pp-130) REVERT: D 195 ASN cc_start: 0.9640 (OUTLIER) cc_final: 0.9097 (t0) REVERT: D 204 MET cc_start: 0.9367 (tpt) cc_final: 0.9048 (tpt) REVERT: D 268 THR cc_start: 0.8953 (p) cc_final: 0.8606 (p) REVERT: D 304 ASN cc_start: 0.9536 (t0) cc_final: 0.9323 (t0) REVERT: D 343 MET cc_start: 0.9075 (mpp) cc_final: 0.8750 (mpp) REVERT: D 588 MET cc_start: 0.7574 (mmm) cc_final: 0.7295 (mmm) REVERT: D 602 GLU cc_start: 0.9201 (mp0) cc_final: 0.8980 (mp0) REVERT: D 710 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.6997 (pmm150) outliers start: 41 outliers final: 14 residues processed: 160 average time/residue: 0.4680 time to fit residues: 84.8242 Evaluate side-chains 140 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 3 optimal weight: 40.0000 chunk 148 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 97 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.138827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.071364 restraints weight = 44345.052| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.21 r_work: 0.2964 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 266 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 307 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14973 Z= 0.137 Angle : 0.691 16.959 20052 Z= 0.319 Chirality : 0.042 0.315 2188 Planarity : 0.004 0.041 2418 Dihedral : 13.752 176.692 2647 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.28 % Allowed : 17.80 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.93 (0.21), residues: 1682 helix: 2.03 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.65 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 55 TYR 0.019 0.001 TYR D 261 PHE 0.032 0.001 PHE D 292 TRP 0.037 0.001 TRP C 25 HIS 0.003 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00301 (14960) covalent geometry : angle 0.68432 (20030) SS BOND : bond 0.00189 ( 2) SS BOND : angle 0.47774 ( 4) hydrogen bonds : bond 0.04052 ( 924) hydrogen bonds : angle 4.15228 ( 2748) Misc. bond : bond 0.00081 ( 5) link_BETA1-3 : bond 0.00512 ( 1) link_BETA1-3 : angle 1.20583 ( 3) link_BETA1-4 : bond 0.00780 ( 1) link_BETA1-4 : angle 2.56174 ( 3) link_NAG-ASN : bond 0.00311 ( 4) link_NAG-ASN : angle 3.66255 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: -0.0329 (OUTLIER) cc_final: -0.0895 (mmt) REVERT: A 382 MET cc_start: 0.3838 (mtm) cc_final: 0.3597 (mmm) REVERT: B 58 MET cc_start: -0.0695 (mmp) cc_final: -0.1831 (mtp) REVERT: B 115 MET cc_start: 0.3826 (mmm) cc_final: 0.3345 (pmm) REVERT: B 172 LEU cc_start: 0.3122 (OUTLIER) cc_final: 0.2814 (mt) REVERT: C 46 MET cc_start: 0.5917 (ptt) cc_final: 0.4565 (pp-130) REVERT: D 195 ASN cc_start: 0.9625 (OUTLIER) cc_final: 0.9053 (t0) REVERT: D 204 MET cc_start: 0.9368 (tpt) cc_final: 0.9058 (tpt) REVERT: D 268 THR cc_start: 0.8921 (p) cc_final: 0.8536 (p) REVERT: D 304 ASN cc_start: 0.9492 (t0) cc_final: 0.9252 (t0) REVERT: D 343 MET cc_start: 0.9097 (mpp) cc_final: 0.8794 (mpp) REVERT: D 588 MET cc_start: 0.7542 (mmm) cc_final: 0.7300 (mmm) REVERT: D 602 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8934 (mp0) REVERT: D 710 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.6954 (pmm150) outliers start: 34 outliers final: 17 residues processed: 154 average time/residue: 0.4456 time to fit residues: 77.8389 Evaluate side-chains 142 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 602 GLU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 141 optimal weight: 0.0770 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.137867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.070002 restraints weight = 44927.192| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.98 r_work: 0.2961 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 307 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 346 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14973 Z= 0.154 Angle : 0.706 16.294 20052 Z= 0.329 Chirality : 0.043 0.320 2188 Planarity : 0.004 0.042 2418 Dihedral : 13.547 176.995 2647 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.14 % Allowed : 17.87 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.90 (0.21), residues: 1682 helix: 2.01 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.66 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 55 TYR 0.022 0.001 TYR D 261 PHE 0.018 0.001 PHE A 283 TRP 0.043 0.001 TRP C 25 HIS 0.004 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00349 (14960) covalent geometry : angle 0.69968 (20030) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.46818 ( 4) hydrogen bonds : bond 0.04061 ( 924) hydrogen bonds : angle 4.19973 ( 2748) Misc. bond : bond 0.00082 ( 5) link_BETA1-3 : bond 0.00321 ( 1) link_BETA1-3 : angle 1.23947 ( 3) link_BETA1-4 : bond 0.00762 ( 1) link_BETA1-4 : angle 2.56255 ( 3) link_NAG-ASN : bond 0.00284 ( 4) link_NAG-ASN : angle 3.57829 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.3500 (mmt) cc_final: 0.3147 (mtm) REVERT: A 382 MET cc_start: 0.3866 (mtm) cc_final: 0.3599 (mmm) REVERT: B 58 MET cc_start: -0.0259 (mmp) cc_final: -0.1434 (mtp) REVERT: B 115 MET cc_start: 0.3797 (mmm) cc_final: 0.3314 (pmm) REVERT: B 172 LEU cc_start: 0.3050 (OUTLIER) cc_final: 0.2728 (mt) REVERT: C 46 MET cc_start: 0.5952 (ptt) cc_final: 0.4590 (pp-130) REVERT: D 195 ASN cc_start: 0.9615 (OUTLIER) cc_final: 0.9094 (t0) REVERT: D 204 MET cc_start: 0.9355 (tpt) cc_final: 0.9049 (tpt) REVERT: D 268 THR cc_start: 0.8934 (p) cc_final: 0.8550 (p) REVERT: D 304 ASN cc_start: 0.9490 (t0) cc_final: 0.9248 (t0) REVERT: D 343 MET cc_start: 0.9094 (mpp) cc_final: 0.8784 (mpp) REVERT: D 588 MET cc_start: 0.7477 (mmm) cc_final: 0.7256 (mmm) REVERT: D 602 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8904 (mp0) REVERT: D 710 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7027 (pmm150) REVERT: F 47 ARG cc_start: 0.8780 (mmt90) cc_final: 0.8565 (mmt180) outliers start: 32 outliers final: 15 residues processed: 153 average time/residue: 0.4751 time to fit residues: 82.2542 Evaluate side-chains 144 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 602 GLU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 137 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 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 195 ASN E 139 HIS F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.137786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.070564 restraints weight = 44731.461| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.02 r_work: 0.2967 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 346 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 379 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 14973 Z= 0.140 Angle : 0.719 15.655 20052 Z= 0.333 Chirality : 0.043 0.336 2188 Planarity : 0.004 0.041 2418 Dihedral : 13.289 177.496 2644 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.74 % Allowed : 18.54 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.91 (0.21), residues: 1682 helix: 2.03 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -0.68 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 55 TYR 0.019 0.001 TYR D 261 PHE 0.020 0.001 PHE D 714 TRP 0.050 0.001 TRP C 25 HIS 0.003 0.000 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00315 (14960) covalent geometry : angle 0.71347 (20030) SS BOND : bond 0.00189 ( 2) SS BOND : angle 0.48156 ( 4) hydrogen bonds : bond 0.04031 ( 924) hydrogen bonds : angle 4.20248 ( 2748) Misc. bond : bond 0.00081 ( 5) link_BETA1-3 : bond 0.00162 ( 1) link_BETA1-3 : angle 1.02576 ( 3) link_BETA1-4 : bond 0.01039 ( 1) link_BETA1-4 : angle 2.42146 ( 3) link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 3.49427 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.3330 (mmt) cc_final: 0.2915 (mtm) REVERT: A 382 MET cc_start: 0.3945 (mtm) cc_final: 0.3665 (mmm) REVERT: B 58 MET cc_start: 0.0007 (mmp) cc_final: -0.1196 (mtp) REVERT: B 115 MET cc_start: 0.3783 (mmm) cc_final: 0.3311 (pmm) REVERT: B 172 LEU cc_start: 0.2969 (OUTLIER) cc_final: 0.2651 (mt) REVERT: C 46 MET cc_start: 0.5924 (ptt) cc_final: 0.4506 (pp-130) REVERT: D 195 ASN cc_start: 0.9618 (OUTLIER) cc_final: 0.9059 (t0) REVERT: D 204 MET cc_start: 0.9357 (tpt) cc_final: 0.9059 (tpt) REVERT: D 212 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9326 (mt) REVERT: D 268 THR cc_start: 0.8900 (p) cc_final: 0.8506 (p) REVERT: D 284 PHE cc_start: 0.9329 (m-80) cc_final: 0.9012 (m-80) REVERT: D 304 ASN cc_start: 0.9478 (t0) cc_final: 0.9243 (t0) REVERT: D 343 MET cc_start: 0.9113 (mpp) cc_final: 0.8790 (mpp) REVERT: D 602 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8891 (mp0) REVERT: D 710 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7029 (pmm150) REVERT: F 47 ARG cc_start: 0.8705 (mmt90) cc_final: 0.8481 (mmt180) outliers start: 26 outliers final: 18 residues processed: 150 average time/residue: 0.5071 time to fit residues: 85.9428 Evaluate side-chains 147 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 602 GLU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 141 optimal weight: 0.0980 chunk 16 optimal weight: 50.0000 chunk 49 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 93 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.137159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.070250 restraints weight = 44530.456| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.84 r_work: 0.2959 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 379 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 406 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14973 Z= 0.161 Angle : 0.742 15.090 20052 Z= 0.346 Chirality : 0.044 0.319 2188 Planarity : 0.004 0.043 2418 Dihedral : 13.213 177.703 2644 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.61 % Allowed : 18.81 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.83 (0.21), residues: 1682 helix: 1.98 (0.15), residues: 1198 sheet: None (None), residues: 0 loop : -0.74 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.023 0.001 TYR D 261 PHE 0.021 0.001 PHE D 714 TRP 0.057 0.001 TRP C 25 HIS 0.004 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00365 (14960) covalent geometry : angle 0.73678 (20030) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.52708 ( 4) hydrogen bonds : bond 0.04093 ( 924) hydrogen bonds : angle 4.24101 ( 2748) Misc. bond : bond 0.00086 ( 5) link_BETA1-3 : bond 0.00419 ( 1) link_BETA1-3 : angle 1.29652 ( 3) link_BETA1-4 : bond 0.00753 ( 1) link_BETA1-4 : angle 2.45918 ( 3) link_NAG-ASN : bond 0.00262 ( 4) link_NAG-ASN : angle 3.44251 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.3328 (mmt) cc_final: 0.2924 (mtm) REVERT: A 382 MET cc_start: 0.3951 (mtm) cc_final: 0.3680 (mmm) REVERT: B 58 MET cc_start: 0.0111 (mmp) cc_final: -0.1124 (mtp) REVERT: B 115 MET cc_start: 0.3769 (mmm) cc_final: 0.3301 (pmm) REVERT: B 172 LEU cc_start: 0.2993 (OUTLIER) cc_final: 0.2670 (mt) REVERT: C 26 MET cc_start: 0.4184 (ttm) cc_final: 0.3826 (mtt) REVERT: C 46 MET cc_start: 0.5945 (ptt) cc_final: 0.4538 (pp-130) REVERT: D 195 ASN cc_start: 0.9635 (OUTLIER) cc_final: 0.9103 (t0) REVERT: D 204 MET cc_start: 0.9381 (tpt) cc_final: 0.9090 (tpt) REVERT: D 268 THR cc_start: 0.8918 (p) cc_final: 0.8533 (p) REVERT: D 304 ASN cc_start: 0.9483 (t0) cc_final: 0.9240 (t0) REVERT: D 343 MET cc_start: 0.9111 (mpp) cc_final: 0.8755 (mmt) REVERT: D 602 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8901 (mp0) REVERT: D 710 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7029 (pmm150) REVERT: F 47 ARG cc_start: 0.8725 (mmt90) cc_final: 0.8501 (mmt180) outliers start: 24 outliers final: 19 residues processed: 142 average time/residue: 0.4922 time to fit residues: 78.9593 Evaluate side-chains 147 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 602 GLU Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 35 optimal weight: 30.0000 chunk 127 optimal weight: 0.0980 chunk 128 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 50.0000 chunk 95 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 83 optimal weight: 9.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.137687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070701 restraints weight = 44255.512| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.80 r_work: 0.2980 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 406 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 414 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14973 Z= 0.128 Angle : 0.730 15.036 20052 Z= 0.338 Chirality : 0.043 0.311 2188 Planarity : 0.004 0.041 2418 Dihedral : 13.074 178.127 2644 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.61 % Allowed : 18.74 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 aren not related in a simple way. whole: 1.85 (0.21), residues: 1682 helix: 1.98 (0.15), residues: 1198 sheet: None (None), residues: 0 loop : -0.71 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.015 0.001 TYR D 261 PHE 0.023 0.001 PHE D 714 TRP 0.044 0.001 TRP C 25 HIS 0.003 0.000 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00280 (14960) covalent geometry : angle 0.72494 (20030) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.57511 ( 4) hydrogen bonds : bond 0.04012 ( 924) hydrogen bonds : angle 4.20294 ( 2748) Misc. bond : bond 0.00079 ( 5) link_BETA1-3 : bond 0.00467 ( 1) link_BETA1-3 : angle 1.03484 ( 3) link_BETA1-4 : bond 0.00716 ( 1) link_BETA1-4 : angle 2.42647 ( 3) link_NAG-ASN : bond 0.00345 ( 4) link_NAG-ASN : angle 3.36023 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9611.45 seconds wall clock time: 163 minutes 33.54 seconds (9813.54 seconds total)