Starting phenix.real_space_refine on Fri Jun 13 04:00:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkp_41356/06_2025/8tkp_41356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkp_41356/06_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_41356/06_2025/8tkp_41356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkp_41356/06_2025/8tkp_41356.map" model { file = "/net/cci-nas-00/data/ceres_data/8tkp_41356/06_2025/8tkp_41356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkp_41356/06_2025/8tkp_41356.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.34, per 1000 atoms: 0.71 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: 4.27 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.47 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: 4.25 Time building geometry restraints manager: 4.95 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 813 or resid 1301 through 1305 or (resid 1307 a \ nd (name 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 or name C33 or name C34 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 62 or resid 201 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: 0.010 Normalize map: mean=0, sd=1: 5.240 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.060 Set scattering table: 0.140 Process input model: 36.330 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (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 TRP 0.008 0.001 TRP D 693 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.001 PHE E 105 TYR 0.037 0.001 TYR A 774 ARG 0.003 0.000 ARG E 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 4) link_NAG-ASN : angle 4.21578 ( 12) link_BETA1-4 : bond 0.00701 ( 1) link_BETA1-4 : angle 3.02954 ( 3) hydrogen bonds : bond 0.11369 ( 924) hydrogen bonds : angle 5.06909 ( 2748) SS BOND : bond 0.00211 ( 2) SS BOND : angle 1.01510 ( 4) link_BETA1-3 : bond 0.00544 ( 1) link_BETA1-3 : angle 0.27173 ( 3) covalent geometry : bond 0.00491 (14960) covalent geometry : angle 0.90850 (20030) Misc. bond : bond 0.00090 ( 5) *********************** 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 : 1.514 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: 0.6084 (mt0) REVERT: B 115 MET cc_start: 0.3999 (mmm) cc_final: 0.3544 (pmm) REVERT: C 53 THR cc_start: 0.6565 (p) cc_final: 0.6219 (t) REVERT: D 157 ASP cc_start: 0.8944 (m-30) cc_final: 0.8507 (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: 1.0989 time to fit residues: 310.2565 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 : 1.612 ------------------------------------------------------------------------------- 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 140 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 763 ASN B 50 ASN D 110 GLN D 130 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 = 0.4561 r_free = 0.4561 target = 0.154049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.086709 restraints weight = 45311.607| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 5.43 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14973 Z= 0.242 Angle : 0.724 11.062 20052 Z= 0.349 Chirality : 0.044 0.350 2188 Planarity : 0.004 0.046 2418 Dihedral : 17.124 179.043 2652 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.08 % Allowed : 13.72 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.21), residues: 1682 helix: 2.18 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -0.71 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 25 HIS 0.009 0.001 HIS A 176 PHE 0.019 0.002 PHE E 109 TYR 0.035 0.002 TYR D 261 ARG 0.007 0.001 ARG D 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 4) link_NAG-ASN : angle 4.81788 ( 12) link_BETA1-4 : bond 0.00426 ( 1) link_BETA1-4 : angle 2.83157 ( 3) hydrogen bonds : bond 0.04736 ( 924) hydrogen bonds : angle 4.34738 ( 2748) SS BOND : bond 0.00991 ( 2) SS BOND : angle 1.15524 ( 4) link_BETA1-3 : bond 0.00309 ( 1) link_BETA1-3 : angle 1.29440 ( 3) covalent geometry : bond 0.00540 (14960) covalent geometry : angle 0.71348 (20030) Misc. bond : bond 0.00117 ( 5) *********************** 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 197 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.551 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: 0.4199 (mtm) cc_final: 0.3908 (mmm) REVERT: B 58 MET cc_start: 0.0757 (mmm) cc_final: 0.0113 (mpp) REVERT: B 115 MET cc_start: 0.3991 (mmm) cc_final: 0.3425 (pmm) REVERT: B 172 LEU cc_start: 0.2862 (OUTLIER) cc_final: 0.2502 (mt) REVERT: D 167 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9416 (tp30) REVERT: D 270 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: D 343 MET cc_start: 0.8838 (mpp) cc_final: 0.8500 (mpp) REVERT: D 588 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7428 (mmm) REVERT: D 710 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7419 (pmm150) REVERT: E 30 ASP cc_start: 0.9181 (p0) cc_final: 0.8574 (OUTLIER) REVERT: E 165 ARG cc_start: 0.9325 (tpp80) cc_final: 0.9091 (tmt170) REVERT: F 54 LYS cc_start: 0.9353 (tptt) cc_final: 0.9044 (tptp) outliers start: 46 outliers final: 12 residues processed: 180 average time/residue: 0.9910 time to fit residues: 201.2421 Evaluate side-chains 134 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TYR 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 270 PHE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 588 MET Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 0.0980 chunk 27 optimal weight: 9.9990 chunk 69 optimal weight: 50.0000 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 79 optimal weight: 50.0000 chunk 37 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.074614 restraints weight = 44012.985| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.22 r_work: 0.3007 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 159 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14973 Z= 0.135 Angle : 0.637 15.421 20052 Z= 0.302 Chirality : 0.041 0.320 2188 Planarity : 0.004 0.043 2418 Dihedral : 15.798 174.769 2647 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.81 % Allowed : 14.26 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1682 helix: 2.12 (0.15), residues: 1198 sheet: None (None), residues: 0 loop : -0.68 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 25 HIS 0.006 0.001 HIS A 176 PHE 0.023 0.001 PHE D 200 TYR 0.058 0.001 TYR A 453 ARG 0.008 0.000 ARG E 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 4) link_NAG-ASN : angle 4.17596 ( 12) link_BETA1-4 : bond 0.00521 ( 1) link_BETA1-4 : angle 2.84578 ( 3) hydrogen bonds : bond 0.04281 ( 924) hydrogen bonds : angle 4.18648 ( 2748) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.88571 ( 4) link_BETA1-3 : bond 0.00438 ( 1) link_BETA1-3 : angle 1.33267 ( 3) covalent geometry : bond 0.00289 (14960) covalent geometry : angle 0.62812 (20030) Misc. bond : bond 0.00076 ( 5) *********************** 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 181 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.770 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: -0.0128 (OUTLIER) cc_final: -0.0691 (mmt) REVERT: A 190 TRP cc_start: 0.8811 (OUTLIER) cc_final: 0.8083 (t-100) REVERT: A 382 MET cc_start: 0.4003 (mtm) cc_final: 0.3739 (mmm) REVERT: B 115 MET cc_start: 0.3967 (mmm) cc_final: 0.3429 (pmm) REVERT: B 172 LEU cc_start: 0.3089 (OUTLIER) cc_final: 0.2785 (mt) REVERT: C 46 MET cc_start: 0.5837 (ptt) cc_final: 0.4783 (pp-130) REVERT: D 114 MET cc_start: 0.9348 (tpt) cc_final: 0.9146 (tpt) REVERT: D 212 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9368 (mt) REVERT: D 268 THR cc_start: 0.8862 (p) cc_final: 0.8547 (p) REVERT: D 284 PHE cc_start: 0.9357 (m-80) cc_final: 0.8943 (m-80) REVERT: D 343 MET cc_start: 0.9078 (mpp) cc_final: 0.8726 (mpp) REVERT: D 710 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7378 (pmm150) REVERT: E 30 ASP cc_start: 0.9307 (p0) cc_final: 0.8755 (OUTLIER) REVERT: F 54 LYS cc_start: 0.9420 (tptt) cc_final: 0.9197 (tptt) outliers start: 42 outliers final: 14 residues processed: 160 average time/residue: 0.9990 time to fit residues: 180.8447 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 : 1.620 ------------------------------------------------------------------------------- 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 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 212 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 665 MET Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 19 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 69 optimal weight: 50.0000 chunk 165 optimal weight: 0.2980 chunk 116 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 50.0000 chunk 66 optimal weight: 7.9990 chunk 19 optimal weight: 0.0070 chunk 134 optimal weight: 0.0980 chunk 50 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN E 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.140333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.072210 restraints weight = 44458.553| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 4.25 r_work: 0.3007 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 159 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14973 Z= 0.116 Angle : 0.614 11.325 20052 Z= 0.289 Chirality : 0.040 0.329 2188 Planarity : 0.004 0.040 2418 Dihedral : 15.013 172.504 2647 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.61 % Allowed : 15.26 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.21), residues: 1682 helix: 2.14 (0.15), residues: 1202 sheet: None (None), residues: 0 loop : -0.71 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 25 HIS 0.004 0.000 HIS A 176 PHE 0.014 0.001 PHE A 283 TYR 0.015 0.001 TYR D 261 ARG 0.008 0.000 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 4) link_NAG-ASN : angle 3.90732 ( 12) link_BETA1-4 : bond 0.00617 ( 1) link_BETA1-4 : angle 2.77068 ( 3) hydrogen bonds : bond 0.04044 ( 924) hydrogen bonds : angle 4.07946 ( 2748) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.73378 ( 4) link_BETA1-3 : bond 0.00328 ( 1) link_BETA1-3 : angle 0.90599 ( 3) covalent geometry : bond 0.00236 (14960) covalent geometry : angle 0.60604 (20030) Misc. bond : bond 0.00071 ( 5) *********************** 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 177 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 1.531 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: A 114 MET cc_start: -0.0279 (OUTLIER) cc_final: -0.0854 (mmt) REVERT: A 382 MET cc_start: 0.3919 (mtm) cc_final: 0.3686 (mmm) REVERT: B 58 MET cc_start: -0.0048 (mpp) cc_final: -0.1021 (mtp) REVERT: B 115 MET cc_start: 0.3784 (mmm) cc_final: 0.3302 (pmm) REVERT: B 172 LEU cc_start: 0.3069 (OUTLIER) cc_final: 0.2768 (mt) REVERT: C 46 MET cc_start: 0.5845 (ptt) cc_final: 0.4623 (pp-130) REVERT: D 114 MET cc_start: 0.9336 (tpt) cc_final: 0.9134 (tpt) REVERT: D 195 ASN cc_start: 0.9555 (OUTLIER) cc_final: 0.9046 (t0) REVERT: D 212 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9328 (mt) REVERT: D 268 THR cc_start: 0.8827 (p) cc_final: 0.8466 (p) REVERT: D 286 ASN cc_start: 0.9459 (m110) cc_final: 0.9228 (m-40) REVERT: D 343 MET cc_start: 0.9107 (mpp) cc_final: 0.8803 (mpp) REVERT: D 588 MET cc_start: 0.8013 (mmm) cc_final: 0.7629 (mmm) REVERT: D 710 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7339 (pmm150) REVERT: E 30 ASP cc_start: 0.9310 (p0) cc_final: 0.8715 (p0) REVERT: E 107 ASP cc_start: 0.9338 (m-30) cc_final: 0.9103 (m-30) REVERT: E 165 ARG cc_start: 0.9394 (tpp80) cc_final: 0.9119 (tmt170) REVERT: F 54 LYS cc_start: 0.9426 (tptt) cc_final: 0.9143 (tptp) outliers start: 39 outliers final: 11 residues processed: 159 average time/residue: 0.9615 time to fit residues: 174.4407 Evaluate side-chains 142 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 134 optimal weight: 0.8980 chunk 4 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 126 optimal weight: 0.0270 chunk 104 optimal weight: 2.9990 overall best weight: 0.4852 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.139459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072208 restraints weight = 44371.473| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.20 r_work: 0.3001 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 209 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 251 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 14973 Z= 0.115 Angle : 0.615 12.390 20052 Z= 0.286 Chirality : 0.040 0.334 2188 Planarity : 0.004 0.040 2418 Dihedral : 14.385 172.104 2647 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.61 % Allowed : 15.73 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.21), residues: 1682 helix: 2.15 (0.15), residues: 1203 sheet: None (None), residues: 0 loop : -0.70 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 190 HIS 0.003 0.000 HIS A 176 PHE 0.019 0.001 PHE D 200 TYR 0.023 0.001 TYR A 453 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 3.77109 ( 12) link_BETA1-4 : bond 0.00628 ( 1) link_BETA1-4 : angle 2.68179 ( 3) hydrogen bonds : bond 0.03933 ( 924) hydrogen bonds : angle 4.06486 ( 2748) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.61356 ( 4) link_BETA1-3 : bond 0.00704 ( 1) link_BETA1-3 : angle 1.07024 ( 3) covalent geometry : bond 0.00240 (14960) covalent geometry : angle 0.60693 (20030) Misc. bond : bond 0.00069 ( 5) *********************** 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 173 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.545 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: -0.0345 (OUTLIER) cc_final: -0.0912 (mmt) REVERT: A 382 MET cc_start: 0.3908 (mtm) cc_final: 0.3681 (mmm) REVERT: B 58 MET cc_start: -0.0288 (mpp) cc_final: -0.1098 (mtp) REVERT: B 115 MET cc_start: 0.3783 (mmm) cc_final: 0.3312 (pmm) REVERT: B 172 LEU cc_start: 0.2966 (OUTLIER) cc_final: 0.2675 (mt) REVERT: C 46 MET cc_start: 0.5846 (ptt) cc_final: 0.4425 (pp-130) REVERT: D 114 MET cc_start: 0.9345 (tpt) cc_final: 0.9132 (tpt) REVERT: D 204 MET cc_start: 0.9378 (tpt) cc_final: 0.9070 (tpt) REVERT: D 212 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9328 (mt) REVERT: D 268 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8407 (p) REVERT: D 286 ASN cc_start: 0.9476 (m110) cc_final: 0.9206 (m-40) REVERT: D 343 MET cc_start: 0.9135 (mpp) cc_final: 0.8824 (mpp) REVERT: D 588 MET cc_start: 0.7898 (mmm) cc_final: 0.7513 (mmm) REVERT: D 710 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.6995 (pmm150) REVERT: E 30 ASP cc_start: 0.9305 (p0) cc_final: 0.8742 (p0) REVERT: E 165 ARG cc_start: 0.9408 (tpp80) cc_final: 0.9120 (tmt170) REVERT: F 54 LYS cc_start: 0.9448 (tptt) cc_final: 0.9163 (tptp) outliers start: 39 outliers final: 11 residues processed: 158 average time/residue: 1.2831 time to fit residues: 230.4667 Evaluate side-chains 140 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 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 212 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 34 optimal weight: 0.0570 chunk 134 optimal weight: 0.0000 chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 141 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 68 optimal weight: 50.0000 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 154 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 overall best weight: 0.3200 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.139486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.072844 restraints weight = 44315.396| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.05 r_work: 0.3015 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 251 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 314 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14973 Z= 0.109 Angle : 0.614 13.800 20052 Z= 0.286 Chirality : 0.040 0.333 2188 Planarity : 0.004 0.039 2418 Dihedral : 13.932 174.536 2647 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.21), residues: 1682 helix: 2.17 (0.15), residues: 1203 sheet: None (None), residues: 0 loop : -0.72 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 25 HIS 0.002 0.000 HIS A 176 PHE 0.017 0.001 PHE D 714 TYR 0.015 0.001 TYR A 453 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 4) link_NAG-ASN : angle 3.64402 ( 12) link_BETA1-4 : bond 0.00774 ( 1) link_BETA1-4 : angle 2.59818 ( 3) hydrogen bonds : bond 0.03815 ( 924) hydrogen bonds : angle 4.06626 ( 2748) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.54993 ( 4) link_BETA1-3 : bond 0.00653 ( 1) link_BETA1-3 : angle 0.95607 ( 3) covalent geometry : bond 0.00220 (14960) covalent geometry : angle 0.60713 (20030) Misc. bond : bond 0.00066 ( 5) *********************** 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: 37 poor density : 136 time to evaluate : 1.576 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: -0.0405 (OUTLIER) cc_final: -0.0989 (mmt) REVERT: A 233 MET cc_start: 0.3576 (mmt) cc_final: 0.3220 (mtm) REVERT: A 382 MET cc_start: 0.3884 (mtm) cc_final: 0.3642 (mmm) REVERT: A 609 MET cc_start: 0.5938 (ppp) cc_final: 0.5233 (ptp) REVERT: B 115 MET cc_start: 0.3799 (mmm) cc_final: 0.3313 (pmm) REVERT: B 172 LEU cc_start: 0.2853 (OUTLIER) cc_final: 0.2547 (mt) REVERT: C 46 MET cc_start: 0.5853 (ptt) cc_final: 0.4375 (pp-130) REVERT: D 195 ASN cc_start: 0.9540 (OUTLIER) cc_final: 0.9062 (t0) REVERT: D 204 MET cc_start: 0.9388 (tpt) cc_final: 0.9075 (tpt) REVERT: D 212 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9341 (mt) REVERT: D 268 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8340 (p) REVERT: D 284 PHE cc_start: 0.9350 (m-80) cc_final: 0.8927 (m-80) REVERT: D 286 ASN cc_start: 0.9478 (m110) cc_final: 0.9206 (m-40) REVERT: D 343 MET cc_start: 0.9147 (mpp) cc_final: 0.8823 (mpp) REVERT: D 588 MET cc_start: 0.7903 (mmm) cc_final: 0.7548 (mmm) REVERT: D 622 ASP cc_start: 0.9436 (m-30) cc_final: 0.9217 (m-30) REVERT: D 710 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.6946 (pmm150) REVERT: D 774 TYR cc_start: 0.7194 (m-10) cc_final: 0.6976 (m-10) REVERT: E 30 ASP cc_start: 0.9302 (p0) cc_final: 0.8773 (p0) REVERT: E 165 ARG cc_start: 0.9397 (tpp80) cc_final: 0.9127 (tmt170) REVERT: F 54 LYS cc_start: 0.9437 (tptt) cc_final: 0.9157 (tptp) outliers start: 37 outliers final: 15 residues processed: 158 average time/residue: 0.9488 time to fit residues: 170.4017 Evaluate side-chains 144 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 16 GLN 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 160 LYS Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 25 optimal weight: 50.0000 chunk 50 optimal weight: 20.0000 chunk 161 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 0.0870 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 50.0000 chunk 118 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- 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 = 0.4471 r_free = 0.4471 target = 0.137620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.070216 restraints weight = 44960.218| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.93 r_work: 0.2974 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 314 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 343 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14973 Z= 0.153 Angle : 0.655 16.495 20052 Z= 0.306 Chirality : 0.042 0.338 2188 Planarity : 0.004 0.041 2418 Dihedral : 13.702 173.047 2647 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.41 % Allowed : 16.67 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.21), residues: 1682 helix: 2.17 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -0.73 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 25 HIS 0.004 0.001 HIS E 198 PHE 0.019 0.001 PHE A 283 TYR 0.026 0.001 TYR D 261 ARG 0.003 0.000 ARG D 625 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 4) link_NAG-ASN : angle 3.55918 ( 12) link_BETA1-4 : bond 0.00851 ( 1) link_BETA1-4 : angle 2.58772 ( 3) hydrogen bonds : bond 0.03967 ( 924) hydrogen bonds : angle 4.14803 ( 2748) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.48630 ( 4) link_BETA1-3 : bond 0.00257 ( 1) link_BETA1-3 : angle 1.20768 ( 3) covalent geometry : bond 0.00342 (14960) covalent geometry : angle 0.64886 (20030) Misc. bond : bond 0.00080 ( 5) *********************** 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 167 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.675 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: -0.0549 (OUTLIER) cc_final: -0.1126 (mmt) REVERT: A 233 MET cc_start: 0.3508 (mmt) cc_final: 0.3098 (mtm) REVERT: A 382 MET cc_start: 0.3906 (mtm) cc_final: 0.3669 (mmm) REVERT: B 115 MET cc_start: 0.3833 (mmm) cc_final: 0.3325 (pmm) REVERT: B 172 LEU cc_start: 0.2809 (OUTLIER) cc_final: 0.2498 (mt) REVERT: C 46 MET cc_start: 0.5874 (ptt) cc_final: 0.4411 (pp-130) REVERT: D 195 ASN cc_start: 0.9593 (OUTLIER) cc_final: 0.9054 (t0) REVERT: D 204 MET cc_start: 0.9389 (tpt) cc_final: 0.9075 (tpt) REVERT: D 212 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9323 (mt) REVERT: D 268 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8479 (p) REVERT: D 270 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8752 (m-10) REVERT: D 343 MET cc_start: 0.9181 (mpp) cc_final: 0.8867 (mpp) REVERT: D 588 MET cc_start: 0.7797 (mmm) cc_final: 0.7462 (mmm) REVERT: D 710 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7202 (pmm150) REVERT: E 30 ASP cc_start: 0.9364 (p0) cc_final: 0.8843 (p0) REVERT: F 47 ARG cc_start: 0.8687 (mmt90) cc_final: 0.8404 (mmt180) REVERT: F 54 LYS cc_start: 0.9435 (tptt) cc_final: 0.9144 (tptp) outliers start: 36 outliers final: 14 residues processed: 153 average time/residue: 1.0271 time to fit residues: 177.5173 Evaluate side-chains 143 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 16 GLN 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 212 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 186 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 119 optimal weight: 0.7980 chunk 156 optimal weight: 0.0870 chunk 155 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.137674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.070932 restraints weight = 44537.666| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.02 r_work: 0.2994 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 343 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 386 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14973 Z= 0.122 Angle : 0.662 18.733 20052 Z= 0.304 Chirality : 0.042 0.325 2188 Planarity : 0.004 0.042 2418 Dihedral : 13.489 174.233 2647 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.74 % Allowed : 17.47 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.21), residues: 1682 helix: 2.12 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -0.70 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 25 HIS 0.002 0.000 HIS E 198 PHE 0.015 0.001 PHE D 714 TYR 0.019 0.001 TYR D 261 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 4) link_NAG-ASN : angle 3.44693 ( 12) link_BETA1-4 : bond 0.00594 ( 1) link_BETA1-4 : angle 2.59159 ( 3) hydrogen bonds : bond 0.03867 ( 924) hydrogen bonds : angle 4.12695 ( 2748) SS BOND : bond 0.00184 ( 2) SS BOND : angle 0.47473 ( 4) link_BETA1-3 : bond 0.00614 ( 1) link_BETA1-3 : angle 1.00944 ( 3) covalent geometry : bond 0.00263 (14960) covalent geometry : angle 0.65652 (20030) Misc. bond : bond 0.00073 ( 5) *********************** 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 158 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.866 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: -0.0518 (OUTLIER) cc_final: -0.1094 (mmt) REVERT: A 233 MET cc_start: 0.3304 (mmt) cc_final: 0.2880 (mtm) REVERT: A 382 MET cc_start: 0.4045 (mtm) cc_final: 0.3820 (mmm) REVERT: A 609 MET cc_start: 0.5672 (ppp) cc_final: 0.4541 (ptp) REVERT: A 678 MET cc_start: 0.5915 (mtp) cc_final: 0.5702 (mpp) REVERT: B 58 MET cc_start: -0.0582 (mmp) cc_final: -0.1347 (mtp) REVERT: B 115 MET cc_start: 0.3845 (mmm) cc_final: 0.3301 (pmm) REVERT: B 172 LEU cc_start: 0.2645 (OUTLIER) cc_final: 0.2316 (mt) REVERT: C 46 MET cc_start: 0.5834 (ptt) cc_final: 0.4316 (pp-130) REVERT: D 195 ASN cc_start: 0.9592 (OUTLIER) cc_final: 0.9065 (t0) REVERT: D 204 MET cc_start: 0.9377 (tpt) cc_final: 0.9070 (tpt) REVERT: D 212 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9323 (mt) REVERT: D 268 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8440 (p) REVERT: D 286 ASN cc_start: 0.9446 (m110) cc_final: 0.9192 (m-40) REVERT: D 343 MET cc_start: 0.9188 (mpp) cc_final: 0.8862 (mpp) REVERT: D 588 MET cc_start: 0.7788 (mmm) cc_final: 0.7481 (mmm) REVERT: D 710 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.6953 (pmm150) REVERT: E 30 ASP cc_start: 0.9349 (p0) cc_final: 0.8840 (p0) REVERT: F 47 ARG cc_start: 0.8647 (mmt90) cc_final: 0.8375 (mmt180) REVERT: F 54 LYS cc_start: 0.9427 (tptt) cc_final: 0.9130 (tptp) outliers start: 26 outliers final: 13 residues processed: 146 average time/residue: 1.2305 time to fit residues: 202.0761 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 : 2.265 ------------------------------------------------------------------------------- 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 16 GLN 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 160 LYS Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 186 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 78 optimal weight: 30.0000 chunk 146 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 96 optimal weight: 0.0770 chunk 7 optimal weight: 30.0000 chunk 4 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 105 optimal weight: 0.0020 chunk 125 optimal weight: 0.0370 chunk 117 optimal weight: 3.9990 overall best weight: 0.2624 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.137472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071267 restraints weight = 44328.126| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.75 r_work: 0.3033 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 386 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 427 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14973 Z= 0.113 Angle : 0.671 20.963 20052 Z= 0.307 Chirality : 0.042 0.322 2188 Planarity : 0.004 0.044 2418 Dihedral : 13.304 174.426 2647 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.74 % Allowed : 17.74 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.21), residues: 1682 helix: 2.12 (0.15), residues: 1207 sheet: None (None), residues: 0 loop : -0.77 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 25 HIS 0.002 0.000 HIS A 176 PHE 0.018 0.001 PHE D 200 TYR 0.012 0.001 TYR D 261 ARG 0.019 0.000 ARG E 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 4) link_NAG-ASN : angle 3.34998 ( 12) link_BETA1-4 : bond 0.00403 ( 1) link_BETA1-4 : angle 2.59558 ( 3) hydrogen bonds : bond 0.03819 ( 924) hydrogen bonds : angle 4.11894 ( 2748) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.44940 ( 4) link_BETA1-3 : bond 0.00371 ( 1) link_BETA1-3 : angle 0.79371 ( 3) covalent geometry : bond 0.00236 (14960) covalent geometry : angle 0.66585 (20030) Misc. bond : bond 0.00065 ( 5) *********************** 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 153 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 2.652 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: -0.0365 (OUTLIER) cc_final: -0.0980 (mmt) REVERT: A 233 MET cc_start: 0.3086 (mmt) cc_final: 0.2596 (mtm) REVERT: A 382 MET cc_start: 0.4025 (mtm) cc_final: 0.3729 (mmm) REVERT: A 609 MET cc_start: 0.5697 (ppp) cc_final: 0.4546 (ptp) REVERT: A 678 MET cc_start: 0.5940 (mtp) cc_final: 0.5689 (mpp) REVERT: B 58 MET cc_start: -0.0326 (mmp) cc_final: -0.1116 (mtp) REVERT: B 115 MET cc_start: 0.3781 (mmm) cc_final: 0.3256 (pmm) REVERT: B 172 LEU cc_start: 0.2311 (OUTLIER) cc_final: 0.1997 (mt) REVERT: C 46 MET cc_start: 0.5848 (ptt) cc_final: 0.4427 (pp-130) REVERT: D 195 ASN cc_start: 0.9541 (OUTLIER) cc_final: 0.9074 (t0) REVERT: D 204 MET cc_start: 0.9387 (tpt) cc_final: 0.9096 (tpt) REVERT: D 212 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9341 (mt) REVERT: D 268 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8365 (p) REVERT: D 284 PHE cc_start: 0.9346 (m-80) cc_final: 0.8942 (m-80) REVERT: D 343 MET cc_start: 0.9173 (mpp) cc_final: 0.8825 (mmt) REVERT: D 588 MET cc_start: 0.7586 (mmm) cc_final: 0.7279 (mmm) REVERT: D 710 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.6885 (pmm150) REVERT: E 30 ASP cc_start: 0.9308 (p0) cc_final: 0.8782 (p0) REVERT: F 47 ARG cc_start: 0.8657 (mmt90) cc_final: 0.8382 (mmt180) REVERT: F 54 LYS cc_start: 0.9439 (tptt) cc_final: 0.9156 (tptp) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 1.2243 time to fit residues: 198.0462 Evaluate side-chains 143 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 16 GLN Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 128 LEU 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 268 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 186 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 86 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 13 optimal weight: 30.0000 chunk 83 optimal weight: 9.9990 chunk 117 optimal weight: 0.1980 chunk 97 optimal weight: 0.0040 chunk 153 optimal weight: 1.9990 chunk 55 optimal weight: 40.0000 chunk 141 optimal weight: 0.0000 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.137108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071986 restraints weight = 44770.187| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.73 r_work: 0.3032 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 427 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 468 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14973 Z= 0.115 Angle : 0.685 21.103 20052 Z= 0.311 Chirality : 0.042 0.323 2188 Planarity : 0.004 0.049 2418 Dihedral : 13.161 174.334 2647 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.47 % Allowed : 18.47 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1682 helix: 2.13 (0.15), residues: 1202 sheet: None (None), residues: 0 loop : -0.75 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP C 25 HIS 0.002 0.000 HIS A 176 PHE 0.016 0.001 PHE A 283 TYR 0.013 0.001 TYR D 261 ARG 0.014 0.000 ARG E 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 4) link_NAG-ASN : angle 3.26386 ( 12) link_BETA1-4 : bond 0.00735 ( 1) link_BETA1-4 : angle 2.47060 ( 3) hydrogen bonds : bond 0.03771 ( 924) hydrogen bonds : angle 4.08330 ( 2748) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.44847 ( 4) link_BETA1-3 : bond 0.00584 ( 1) link_BETA1-3 : angle 0.87984 ( 3) covalent geometry : bond 0.00243 (14960) covalent geometry : angle 0.67962 (20030) Misc. bond : bond 0.00064 ( 5) ********************** 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 155 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.651 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: -0.0299 (OUTLIER) cc_final: -0.0890 (mmt) REVERT: A 202 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4823 (pmt) REVERT: A 233 MET cc_start: 0.3286 (mmt) cc_final: 0.2854 (mtm) REVERT: A 382 MET cc_start: 0.4038 (mtm) cc_final: 0.3729 (mmm) REVERT: A 609 MET cc_start: 0.5800 (ppp) cc_final: 0.4612 (ptp) REVERT: B 58 MET cc_start: -0.0415 (mmp) cc_final: -0.1038 (mtp) REVERT: B 115 MET cc_start: 0.3801 (mmm) cc_final: 0.3261 (pmm) REVERT: B 172 LEU cc_start: 0.2367 (OUTLIER) cc_final: 0.2034 (mt) REVERT: C 46 MET cc_start: 0.5774 (ptt) cc_final: 0.4220 (pp-130) REVERT: D 195 ASN cc_start: 0.9547 (OUTLIER) cc_final: 0.9086 (t0) REVERT: D 204 MET cc_start: 0.9414 (tpt) cc_final: 0.9132 (tpt) REVERT: D 268 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8361 (p) REVERT: D 284 PHE cc_start: 0.9341 (m-80) cc_final: 0.8976 (m-80) REVERT: D 343 MET cc_start: 0.9181 (mpp) cc_final: 0.8833 (mmt) REVERT: D 588 MET cc_start: 0.7438 (mmm) cc_final: 0.7116 (mmm) REVERT: D 710 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7745 (mtt180) REVERT: F 47 ARG cc_start: 0.8639 (mmt90) cc_final: 0.8369 (mmt180) REVERT: F 54 LYS cc_start: 0.9422 (tptt) cc_final: 0.9162 (tptp) outliers start: 22 outliers final: 11 residues processed: 147 average time/residue: 1.0156 time to fit residues: 168.9752 Evaluate side-chains 135 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 202 MET 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 16 GLN 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 268 THR Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 186 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 116 optimal weight: 0.9980 chunk 2 optimal weight: 30.0000 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 30.0000 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.135819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.070491 restraints weight = 44987.662| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.54 r_work: 0.3010 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 468 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 482 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14973 Z= 0.138 Angle : 0.696 20.503 20052 Z= 0.322 Chirality : 0.043 0.324 2188 Planarity : 0.004 0.049 2418 Dihedral : 13.074 174.605 2647 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.34 % Allowed : 18.41 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.21), residues: 1682 helix: 2.13 (0.15), residues: 1202 sheet: None (None), residues: 0 loop : -0.75 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP C 25 HIS 0.003 0.000 HIS E 198 PHE 0.019 0.001 PHE D 200 TYR 0.023 0.001 TYR D 261 ARG 0.014 0.000 ARG E 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 4) link_NAG-ASN : angle 3.18907 ( 12) link_BETA1-4 : bond 0.00675 ( 1) link_BETA1-4 : angle 2.50314 ( 3) hydrogen bonds : bond 0.03865 ( 924) hydrogen bonds : angle 4.13966 ( 2748) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.44602 ( 4) link_BETA1-3 : bond 0.00304 ( 1) link_BETA1-3 : angle 1.01370 ( 3) covalent geometry : bond 0.00307 (14960) covalent geometry : angle 0.69120 (20030) Misc. bond : bond 0.00079 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18735.82 seconds wall clock time: 326 minutes 18.35 seconds (19578.35 seconds total)