Starting phenix.real_space_refine on Fri Jul 3 14:43:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkp_41356/07_2026/8tkp_41356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkp_41356/07_2026/8tkp_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tkp_41356/07_2026/8tkp_41356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkp_41356/07_2026/8tkp_41356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tkp_41356/07_2026/8tkp_41356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkp_41356/07_2026/8tkp_41356.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 10 5.49 5 S 74 5.16 5 C 9731 2.51 5 N 2347 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14666 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4992 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 378 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 4992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4992 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 378 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 291 Unusual residues: {'CLR': 1, 'NAG': 1, 'PEE': 4, 'R16': 9, 'TWT': 2} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 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: 2.89, per 1000 atoms: 0.20 Number of scatterers: 14666 At special positions: 0 Unit cell: (139.608, 111.354, 112.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 74 16.00 P 10 15.00 O 2500 8.00 N 2347 7.00 C 9731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 594 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS D 594 " - pdb=" SG CYS D 743 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied BETA1-3 " NAG H 1 " - " NAG H 2 " BETA1-4 " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1316 " - " ASN A 748 " " NAG D1316 " - " ASN D 748 " " NAG G 1 " - " ASN A 225 " " NAG H 1 " - " ASN D 225 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 607.6 milliseconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 4 sheets defined 76.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 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: 1.94 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2170 1.30 - 1.43: 3945 1.43 - 1.55: 8703 1.55 - 1.68: 20 1.68 - 1.81: 122 Bond restraints: 14960 Sorted by residual: bond pdb=" CA SER A 775 " pdb=" C SER A 775 " ideal model delta sigma weight residual 1.524 1.452 0.072 1.26e-02 6.30e+03 3.26e+01 bond pdb=" C ASN A 770 " pdb=" O ASN A 770 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.92e+01 bond pdb=" N LYS A 766 " pdb=" CA LYS A 766 " ideal model delta sigma weight residual 1.456 1.405 0.051 1.23e-02 6.61e+03 1.75e+01 bond pdb=" CA LYS A 766 " pdb=" C LYS A 766 " ideal model delta sigma weight residual 1.524 1.473 0.050 1.26e-02 6.30e+03 1.59e+01 bond pdb=" N GLN A 807 " pdb=" CA GLN A 807 " ideal model delta sigma weight residual 1.459 1.414 0.044 1.16e-02 7.43e+03 1.47e+01 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 19793 3.35 - 6.71: 187 6.71 - 10.06: 38 10.06 - 13.42: 2 13.42 - 16.77: 10 Bond angle restraints: 20030 Sorted by residual: angle pdb=" N TYR A 774 " pdb=" CA TYR A 774 " pdb=" C TYR A 774 " ideal model delta sigma weight residual 111.28 104.44 6.84 1.09e+00 8.42e-01 3.93e+01 angle pdb=" C VAL A 769 " pdb=" CA VAL A 769 " pdb=" CB VAL A 769 " ideal model delta sigma weight residual 112.14 104.18 7.96 1.35e+00 5.49e-01 3.47e+01 angle pdb=" N GLN A 807 " pdb=" CA GLN A 807 " pdb=" C GLN A 807 " ideal model delta sigma weight residual 111.02 104.02 7.00 1.22e+00 6.72e-01 3.29e+01 angle pdb=" O3P PEE A1311 " pdb=" P PEE A1311 " pdb=" O4P PEE A1311 " ideal model delta sigma weight residual 92.91 109.68 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O3P PEE A1302 " pdb=" P PEE A1302 " pdb=" O4P PEE A1302 " ideal model delta sigma weight residual 92.91 109.62 -16.71 3.00e+00 1.11e-01 3.10e+01 ... (remaining 20025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 8961 35.57 - 71.14: 191 71.14 - 106.71: 43 106.71 - 142.29: 13 142.29 - 177.86: 10 Dihedral angle restraints: 9218 sinusoidal: 4242 harmonic: 4976 Sorted by residual: dihedral pdb=" C ASN A 763 " pdb=" N ASN A 763 " pdb=" CA ASN A 763 " pdb=" CB ASN A 763 " ideal model delta harmonic sigma weight residual -122.60 -138.81 16.21 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" N ASN A 763 " pdb=" C ASN A 763 " pdb=" CA ASN A 763 " pdb=" CB ASN A 763 " ideal model delta harmonic sigma weight residual 122.80 136.16 -13.36 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" C TYR A 774 " pdb=" N TYR A 774 " pdb=" CA TYR A 774 " pdb=" CB TYR A 774 " ideal model delta harmonic sigma weight residual -122.60 -110.09 -12.51 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 9215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2167 0.158 - 0.316: 16 0.316 - 0.473: 4 0.473 - 0.631: 0 0.631 - 0.789: 1 Chirality restraints: 2188 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O3 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.10e+01 chirality pdb=" CA ASN A 763 " pdb=" N ASN A 763 " pdb=" C ASN A 763 " pdb=" CB ASN A 763 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CA VAL A 799 " pdb=" N VAL A 799 " pdb=" C VAL A 799 " pdb=" CB VAL A 799 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 2185 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1316 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A1316 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A1316 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG A1316 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1316 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.306 2.00e-02 2.50e+03 2.59e-01 8.37e+02 pdb=" C7 NAG H 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.259 2.00e-02 2.50e+03 2.19e-01 5.97e+02 pdb=" C7 NAG G 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.370 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.005 2.00e-02 2.50e+03 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 8 1.90 - 2.65: 245 2.65 - 3.40: 20861 3.40 - 4.15: 33853 4.15 - 4.90: 63441 Nonbonded interactions: 118408 Sorted by model distance: nonbonded pdb=" CA GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.152 3.470 nonbonded pdb=" CA GLN A 804 " pdb=" CD GLN A 807 " model vdw 1.243 3.700 nonbonded pdb=" C GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.305 3.270 nonbonded pdb=" CD1 LEU A 809 " pdb=" CD2 LEU D 809 " model vdw 1.586 3.880 nonbonded pdb=" O GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.603 3.040 ... (remaining 118403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 89 through 1305 or (resid 1307 and (name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 40 or name C41)) or (resid 1308 and (name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name C37)) or resid 1309 through 1316)) selection = (chain 'D' and (resid 89 through 813 or (resid 1301 and (name C1 or name C10 or \ name C11 or name C12 or name C2 or name C3 or name C4 or name C5 or name C6 or n \ ame C7 or name C8 or name C9 )) or resid 1302 through 1305 or (resid 1307 and (n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41)) or (resid 1308 and (name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37)) or (resid 1309 and \ (name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C40 or name C41 or name C42)) or (resid 1310 and (name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C40 or name C41 or name C42)) or resid 1311 through 1316)) } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 15 through 204) selection = (chain 'F' and (resid 15 through 62 or (resid 201 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or \ name C8 or name C9 )) or (resid 202 and (name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41)) or (resid 203 and (name C31 or name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 204 and (name CA or name C1 or name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O2 )))) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.16 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.550 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14973 Z= 0.285 Angle : 0.915 16.771 20052 Z= 0.413 Chirality : 0.048 0.789 2188 Planarity : 0.011 0.295 2418 Dihedral : 16.841 177.858 5992 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.94 % Allowed : 6.89 % Favored : 92.17 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.21), residues: 1682 helix: 2.40 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 195 TYR 0.037 0.001 TYR A 774 PHE 0.015 0.001 PHE E 105 TRP 0.008 0.001 TRP D 693 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.28 (14960) covalent geometry : angle 0.90850 / 0.41 (20030) SS BOND : bond 0.00211 / 0.10 ( 2) SS BOND : angle 1.01510 / 0.57 ( 4) hydrogen bonds : bond 0.11369 / 7.38 ( 924) hydrogen bonds : angle 5.06909 / 3.65 ( 2748) Misc. bond : bond 0.00090 / 0.05 ( 5) link_BETA1-3 : bond 0.00544 / 0.29 ( 1) link_BETA1-3 : angle 0.27173 / 0.16 ( 3) link_BETA1-4 : bond 0.00701 / 0.37 ( 1) link_BETA1-4 : angle 3.02954 / 1.58 ( 3) link_NAG-ASN : bond 0.00654 / 0.33 ( 4) link_NAG-ASN : angle 4.21578 / 2.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.1542 (mtm) cc_final: 0.1256 (mmm) REVERT: A 807 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6083 (mt0) REVERT: B 115 MET cc_start: 0.3999 (mmm) cc_final: 0.3544 (pmm) REVERT: C 26 MET cc_start: 0.1734 (mtp) cc_final: 0.1530 (ttm) REVERT: C 53 THR cc_start: 0.6565 (p) cc_final: 0.6220 (t) REVERT: D 157 ASP cc_start: 0.8944 (m-30) cc_final: 0.8485 (m-30) REVERT: D 292 PHE cc_start: 0.9182 (t80) cc_final: 0.8944 (t80) REVERT: D 437 LEU cc_start: 0.9460 (tp) cc_final: 0.9238 (tm) REVERT: D 710 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7554 (pmm150) REVERT: F 54 LYS cc_start: 0.9202 (tptt) cc_final: 0.8781 (tptt) outliers start: 14 outliers final: 3 residues processed: 253 average time/residue: 0.4357 time to fit residues: 123.2864 Evaluate side-chains 139 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain E residue 95 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 ASN A 655 ASN A 763 ASN B 50 ASN D 110 GLN D 358 GLN D 590 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.157077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.092201 restraints weight = 44458.693| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 5.19 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 139 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (11 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14973 Z= 0.137 Angle : 0.658 10.793 20052 Z= 0.315 Chirality : 0.041 0.335 2188 Planarity : 0.004 0.044 2418 Dihedral : 17.126 175.492 2652 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.41 % Allowed : 13.86 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.21), residues: 1682 helix: 2.30 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -0.71 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 238 TYR 0.030 0.001 TYR A 774 PHE 0.023 0.001 PHE A 732 TRP 0.014 0.001 TRP C 25 HIS 0.009 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (14960) covalent geometry : angle 0.64712 / 0.31 (20030) SS BOND : bond 0.02955 / 1.55 ( 2) SS BOND : angle 1.43609 / 0.84 ( 4) hydrogen bonds : bond 0.04604 / 3.10 ( 924) hydrogen bonds : angle 4.21734 / 3.02 ( 2748) Misc. bond : bond 0.00060 / 0.03 ( 5) link_BETA1-3 : bond 0.00209 / 0.11 ( 1) link_BETA1-3 : angle 2.15358 / 1.16 ( 3) link_BETA1-4 : bond 0.00706 / 0.37 ( 1) link_BETA1-4 : angle 2.60989 / 1.36 ( 3) link_NAG-ASN : bond 0.00562 / 0.29 ( 4) link_NAG-ASN : angle 4.47458 / 2.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.440 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: A 382 MET cc_start: 0.4168 (mtm) cc_final: 0.3897 (mmm) REVERT: A 678 MET cc_start: 0.6430 (mmm) cc_final: 0.6225 (mmm) REVERT: B 58 MET cc_start: -0.0037 (mmm) cc_final: -0.0839 (mpp) REVERT: B 115 MET cc_start: 0.3905 (mmm) cc_final: 0.3407 (pmm) REVERT: B 172 LEU cc_start: 0.3186 (OUTLIER) cc_final: 0.2851 (mt) REVERT: D 157 ASP cc_start: 0.9260 (m-30) cc_final: 0.9005 (m-30) REVERT: D 343 MET cc_start: 0.8669 (mpp) cc_final: 0.8334 (mpp) REVERT: D 395 THR cc_start: 0.9285 (p) cc_final: 0.9074 (t) REVERT: D 588 MET cc_start: 0.8088 (mmm) cc_final: 0.7589 (mmm) REVERT: D 710 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7315 (pmm150) REVERT: F 54 LYS cc_start: 0.9390 (tptt) cc_final: 0.9096 (tptp) outliers start: 36 outliers final: 6 residues processed: 173 average time/residue: 0.4060 time to fit residues: 79.5707 Evaluate side-chains 132 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 36 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.145379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075521 restraints weight = 44724.179| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.73 r_work: 0.3003 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 139 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 161 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14973 Z= 0.158 Angle : 0.652 14.998 20052 Z= 0.311 Chirality : 0.042 0.349 2188 Planarity : 0.004 0.041 2418 Dihedral : 15.697 178.693 2644 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.68 % Allowed : 13.92 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.21), residues: 1682 helix: 2.14 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -0.70 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 97 TYR 0.028 0.001 TYR D 261 PHE 0.024 0.001 PHE D 200 TRP 0.021 0.001 TRP C 25 HIS 0.006 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (14960) covalent geometry : angle 0.64314 / 0.31 (20030) SS BOND : bond 0.00316 / 0.16 ( 2) SS BOND : angle 0.80894 / 0.45 ( 4) hydrogen bonds : bond 0.04297 / 2.90 ( 924) hydrogen bonds : angle 4.16676 / 2.99 ( 2748) Misc. bond : bond 0.00079 / 0.04 ( 5) link_BETA1-3 : bond 0.00114 / 0.06 ( 1) link_BETA1-3 : angle 1.30703 / 0.66 ( 3) link_BETA1-4 : bond 0.00853 / 0.45 ( 1) link_BETA1-4 : angle 2.86051 / 1.49 ( 3) link_NAG-ASN : bond 0.00397 / 0.20 ( 4) link_NAG-ASN : angle 4.02535 / 2.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.465 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: -0.0210 (OUTLIER) cc_final: -0.0693 (mmt) REVERT: A 190 TRP cc_start: 0.8784 (OUTLIER) cc_final: 0.8081 (t-100) REVERT: A 382 MET cc_start: 0.3950 (mtm) cc_final: 0.3735 (mmm) REVERT: B 115 MET cc_start: 0.3867 (mmm) cc_final: 0.3408 (pmm) REVERT: B 172 LEU cc_start: 0.3478 (OUTLIER) cc_final: 0.3214 (mt) REVERT: C 46 MET cc_start: 0.5727 (ptt) cc_final: 0.4789 (pp-130) REVERT: D 439 PHE cc_start: 0.9690 (OUTLIER) cc_final: 0.9330 (m-80) REVERT: D 588 MET cc_start: 0.8014 (mmm) cc_final: 0.7605 (mmm) REVERT: D 622 ASP cc_start: 0.9511 (m-30) cc_final: 0.9197 (m-30) REVERT: D 710 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7098 (pmm150) REVERT: F 54 LYS cc_start: 0.9453 (tptt) cc_final: 0.9185 (tptp) outliers start: 40 outliers final: 10 residues processed: 162 average time/residue: 0.3967 time to fit residues: 73.0172 Evaluate side-chains 136 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 0 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 chunk 109 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 121 optimal weight: 0.0000 chunk 22 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.142214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.073090 restraints weight = 44807.180| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.16 r_work: 0.2989 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 161 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14973 Z= 0.152 Angle : 0.643 11.511 20052 Z= 0.306 Chirality : 0.041 0.328 2188 Planarity : 0.004 0.048 2418 Dihedral : 15.115 172.197 2644 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.34 % Allowed : 15.19 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.21), residues: 1682 helix: 2.07 (0.15), residues: 1202 sheet: None (None), residues: 0 loop : -0.79 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 62 TYR 0.025 0.001 TYR D 261 PHE 0.020 0.001 PHE A 283 TRP 0.021 0.001 TRP C 25 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (14960) covalent geometry : angle 0.63454 / 0.30 (20030) SS BOND : bond 0.00321 / 0.16 ( 2) SS BOND : angle 0.70596 / 0.39 ( 4) hydrogen bonds : bond 0.04216 / 2.85 ( 924) hydrogen bonds : angle 4.17186 / 3.01 ( 2748) Misc. bond : bond 0.00078 / 0.04 ( 5) link_BETA1-3 : bond 0.00359 / 0.19 ( 1) link_BETA1-3 : angle 1.29472 / 0.66 ( 3) link_BETA1-4 : bond 0.00664 / 0.35 ( 1) link_BETA1-4 : angle 2.77565 / 1.45 ( 3) link_NAG-ASN : bond 0.00363 / 0.19 ( 4) link_NAG-ASN : angle 3.91720 / 2.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.380 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: B 115 MET cc_start: 0.3835 (mmm) cc_final: 0.3405 (pmm) REVERT: B 172 LEU cc_start: 0.3338 (OUTLIER) cc_final: 0.3071 (mt) REVERT: C 46 MET cc_start: 0.5695 (ptt) cc_final: 0.4617 (pp-130) REVERT: D 195 ASN cc_start: 0.9592 (OUTLIER) cc_final: 0.9053 (t0) REVERT: D 268 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8554 (p) REVERT: D 343 MET cc_start: 0.8996 (mpp) cc_final: 0.8665 (mpp) REVERT: D 588 MET cc_start: 0.7922 (mmm) cc_final: 0.7528 (mmm) REVERT: D 622 ASP cc_start: 0.9496 (m-30) cc_final: 0.9027 (m-30) REVERT: D 710 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7032 (pmm150) REVERT: F 54 LYS cc_start: 0.9451 (tptt) cc_final: 0.9161 (tptp) outliers start: 35 outliers final: 11 residues processed: 155 average time/residue: 0.3707 time to fit residues: 65.2888 Evaluate side-chains 137 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 18 VAL 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 31 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 50.0000 chunk 144 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.140792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071915 restraints weight = 44447.515| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.14 r_work: 0.2968 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 207 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 249 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14973 Z= 0.166 Angle : 0.641 10.950 20052 Z= 0.307 Chirality : 0.041 0.328 2188 Planarity : 0.004 0.039 2418 Dihedral : 14.431 173.358 2644 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.81 % Allowed : 15.39 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.21), residues: 1682 helix: 2.03 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.81 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 62 TYR 0.028 0.001 TYR D 261 PHE 0.024 0.001 PHE D 200 TRP 0.040 0.001 TRP A 190 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (14960) covalent geometry : angle 0.63390 / 0.30 (20030) SS BOND : bond 0.00299 / 0.15 ( 2) SS BOND : angle 0.62654 / 0.34 ( 4) hydrogen bonds : bond 0.04123 / 2.79 ( 924) hydrogen bonds : angle 4.12881 / 2.98 ( 2748) Misc. bond : bond 0.00083 / 0.04 ( 5) link_BETA1-3 : bond 0.00142 / 0.07 ( 1) link_BETA1-3 : angle 1.37024 / 0.70 ( 3) link_BETA1-4 : bond 0.00810 / 0.43 ( 1) link_BETA1-4 : angle 2.70530 / 1.42 ( 3) link_NAG-ASN : bond 0.00341 / 0.18 ( 4) link_NAG-ASN : angle 3.78036 / 1.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.643 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: -0.0385 (OUTLIER) cc_final: -0.0925 (mmt) REVERT: A 609 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.5541 (ptm) REVERT: B 115 MET cc_start: 0.3775 (mmm) cc_final: 0.3327 (pmm) REVERT: B 172 LEU cc_start: 0.3305 (OUTLIER) cc_final: 0.3036 (mt) REVERT: C 26 MET cc_start: 0.3072 (ttm) cc_final: 0.2743 (mtt) REVERT: C 46 MET cc_start: 0.5734 (ptt) cc_final: 0.4520 (pp-130) REVERT: D 195 ASN cc_start: 0.9603 (OUTLIER) cc_final: 0.9062 (t0) REVERT: D 268 THR cc_start: 0.8910 (p) cc_final: 0.8578 (p) REVERT: D 343 MET cc_start: 0.9023 (mpp) cc_final: 0.8692 (mpp) REVERT: D 588 MET cc_start: 0.7920 (mmm) cc_final: 0.7589 (mmm) REVERT: D 622 ASP cc_start: 0.9522 (m-30) cc_final: 0.9057 (m-30) REVERT: D 710 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7000 (pmm150) REVERT: E 165 ARG cc_start: 0.9439 (tpp80) cc_final: 0.9114 (tmt170) REVERT: F 54 LYS cc_start: 0.9430 (tptt) cc_final: 0.9164 (tptp) outliers start: 42 outliers final: 15 residues processed: 156 average time/residue: 0.3714 time to fit residues: 66.2122 Evaluate side-chains 142 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 609 MET Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 123 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 40.0000 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 138 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS 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 = 0.139245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.069903 restraints weight = 45084.663| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.49 r_work: 0.2942 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 249 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 286 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14973 Z= 0.198 Angle : 0.665 14.554 20052 Z= 0.317 Chirality : 0.042 0.324 2188 Planarity : 0.004 0.044 2418 Dihedral : 14.054 175.259 2644 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.74 % Allowed : 15.93 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.21), residues: 1682 helix: 1.98 (0.15), residues: 1205 sheet: None (None), residues: 0 loop : -0.84 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 625 TYR 0.030 0.001 TYR D 261 PHE 0.016 0.001 PHE E 109 TRP 0.034 0.001 TRP C 25 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (14960) covalent geometry : angle 0.65794 / 0.32 (20030) SS BOND : bond 0.00279 / 0.14 ( 2) SS BOND : angle 0.53689 / 0.29 ( 4) hydrogen bonds : bond 0.04125 / 2.79 ( 924) hydrogen bonds : angle 4.16082 / 3.00 ( 2748) Misc. bond : bond 0.00092 / 0.05 ( 5) link_BETA1-3 : bond 0.00192 / 0.10 ( 1) link_BETA1-3 : angle 1.55005 / 0.79 ( 3) link_BETA1-4 : bond 0.01350 / 0.71 ( 1) link_BETA1-4 : angle 2.48810 / 1.30 ( 3) link_NAG-ASN : bond 0.00386 / 0.20 ( 4) link_NAG-ASN : angle 3.73265 / 1.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.677 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: -0.0397 (OUTLIER) cc_final: -0.0930 (mmt) REVERT: A 233 MET cc_start: 0.3651 (mmt) cc_final: 0.3341 (mtm) REVERT: A 382 MET cc_start: 0.3149 (ttp) cc_final: 0.2848 (ppp) REVERT: A 609 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5326 (ptm) REVERT: B 58 MET cc_start: -0.0838 (mmp) cc_final: -0.1786 (mtp) REVERT: B 115 MET cc_start: 0.3791 (mmm) cc_final: 0.3337 (pmm) REVERT: B 172 LEU cc_start: 0.3147 (OUTLIER) cc_final: 0.2859 (mt) REVERT: C 46 MET cc_start: 0.5745 (ptt) cc_final: 0.4394 (pp-130) REVERT: D 195 ASN cc_start: 0.9633 (OUTLIER) cc_final: 0.9077 (t0) REVERT: D 204 MET cc_start: 0.9362 (tpt) cc_final: 0.9047 (tpt) REVERT: D 268 THR cc_start: 0.8938 (p) cc_final: 0.8590 (p) REVERT: D 270 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8673 (m-10) REVERT: D 343 MET cc_start: 0.9142 (mpp) cc_final: 0.8772 (mmt) REVERT: D 588 MET cc_start: 0.7802 (mmm) cc_final: 0.7516 (mmm) REVERT: D 710 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7008 (pmm150) REVERT: E 165 ARG cc_start: 0.9443 (tpp80) cc_final: 0.9116 (tmt170) REVERT: F 54 LYS cc_start: 0.9426 (tptt) cc_final: 0.9138 (tptp) outliers start: 41 outliers final: 16 residues processed: 162 average time/residue: 0.4084 time to fit residues: 75.3561 Evaluate side-chains 144 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 609 MET Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 18 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 63 optimal weight: 20.0000 chunk 116 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 3 optimal weight: 40.0000 chunk 148 optimal weight: 0.5980 chunk 0 optimal weight: 50.0000 chunk 97 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 655 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.139356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.071692 restraints weight = 44316.253| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.01 r_work: 0.2981 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 286 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 316 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14973 Z= 0.131 Angle : 0.663 15.532 20052 Z= 0.309 Chirality : 0.041 0.330 2188 Planarity : 0.004 0.039 2418 Dihedral : 13.666 176.585 2644 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.07 % Allowed : 16.73 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.21), residues: 1682 helix: 2.01 (0.15), residues: 1205 sheet: None (None), residues: 0 loop : -0.83 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.018 0.001 TYR D 261 PHE 0.031 0.001 PHE D 292 TRP 0.038 0.001 TRP C 25 HIS 0.003 0.000 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14960) covalent geometry : angle 0.65669 / 0.31 (20030) SS BOND : bond 0.00200 / 0.10 ( 2) SS BOND : angle 0.48093 / 0.26 ( 4) hydrogen bonds : bond 0.04003 / 2.70 ( 924) hydrogen bonds : angle 4.09881 / 2.97 ( 2748) Misc. bond : bond 0.00074 / 0.04 ( 5) link_BETA1-3 : bond 0.00482 / 0.25 ( 1) link_BETA1-3 : angle 1.12651 / 0.59 ( 3) link_BETA1-4 : bond 0.00698 / 0.37 ( 1) link_BETA1-4 : angle 2.57944 / 1.35 ( 3) link_NAG-ASN : bond 0.00313 / 0.16 ( 4) link_NAG-ASN : angle 3.59790 / 1.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.344 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 202 MET cc_start: 0.4821 (OUTLIER) cc_final: 0.4323 (pmt) REVERT: A 233 MET cc_start: 0.3426 (mmt) cc_final: 0.3057 (mtm) REVERT: A 382 MET cc_start: 0.3138 (ttp) cc_final: 0.2815 (ppp) REVERT: B 58 MET cc_start: -0.0742 (mmp) cc_final: -0.1698 (mtp) REVERT: B 115 MET cc_start: 0.3832 (mmm) cc_final: 0.3350 (pmm) REVERT: B 172 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2745 (mt) REVERT: C 46 MET cc_start: 0.5739 (ptt) cc_final: 0.4389 (pp-130) REVERT: D 114 MET cc_start: 0.9239 (tpt) cc_final: 0.9020 (tpt) REVERT: D 195 ASN cc_start: 0.9622 (OUTLIER) cc_final: 0.9033 (t0) REVERT: D 204 MET cc_start: 0.9342 (tpt) cc_final: 0.9041 (tpt) REVERT: D 268 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8506 (p) REVERT: D 284 PHE cc_start: 0.9295 (m-80) cc_final: 0.8923 (m-80) REVERT: D 343 MET cc_start: 0.9155 (mpp) cc_final: 0.8796 (mmt) REVERT: D 588 MET cc_start: 0.7684 (mmm) cc_final: 0.7426 (mmm) REVERT: D 710 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.6859 (pmm150) REVERT: E 165 ARG cc_start: 0.9437 (tpp80) cc_final: 0.9113 (tmt170) REVERT: F 26 MET cc_start: 0.8864 (pmm) cc_final: 0.8249 (pmm) outliers start: 31 outliers final: 7 residues processed: 153 average time/residue: 0.4104 time to fit residues: 70.7559 Evaluate side-chains 136 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 0.0470 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.138729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.070727 restraints weight = 44919.517| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 4.08 r_work: 0.2964 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 316 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 362 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3279 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= 0.147 Angle : 0.681 18.976 20052 Z= 0.318 Chirality : 0.042 0.319 2188 Planarity : 0.004 0.043 2418 Dihedral : 13.449 176.807 2644 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.67 % Allowed : 17.27 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.21), residues: 1682 helix: 2.04 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.79 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 625 TYR 0.021 0.001 TYR D 261 PHE 0.016 0.001 PHE A 283 TRP 0.046 0.001 TRP C 25 HIS 0.004 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (14960) covalent geometry : angle 0.67497 / 0.32 (20030) SS BOND : bond 0.00223 / 0.11 ( 2) SS BOND : angle 0.47778 / 0.26 ( 4) hydrogen bonds : bond 0.03965 / 2.68 ( 924) hydrogen bonds : angle 4.12948 / 3.00 ( 2748) Misc. bond : bond 0.00079 / 0.04 ( 5) link_BETA1-3 : bond 0.00446 / 0.23 ( 1) link_BETA1-3 : angle 1.27771 / 0.66 ( 3) link_BETA1-4 : bond 0.00799 / 0.42 ( 1) link_BETA1-4 : angle 2.52321 / 1.32 ( 3) link_NAG-ASN : bond 0.00277 / 0.14 ( 4) link_NAG-ASN : angle 3.49490 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.594 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 202 MET cc_start: 0.4211 (OUTLIER) cc_final: 0.3848 (pmt) REVERT: A 233 MET cc_start: 0.3378 (mmt) cc_final: 0.3044 (mtm) REVERT: A 382 MET cc_start: 0.3106 (OUTLIER) cc_final: 0.2816 (ppp) REVERT: B 58 MET cc_start: -0.0633 (mmp) cc_final: -0.1575 (mtp) REVERT: B 115 MET cc_start: 0.3793 (mmm) cc_final: 0.3329 (pmm) REVERT: B 172 LEU cc_start: 0.3023 (OUTLIER) cc_final: 0.2698 (mt) REVERT: C 46 MET cc_start: 0.5800 (ptt) cc_final: 0.4409 (pp-130) REVERT: D 195 ASN cc_start: 0.9638 (OUTLIER) cc_final: 0.9039 (t0) REVERT: D 204 MET cc_start: 0.9363 (tpt) cc_final: 0.9073 (tpt) REVERT: D 268 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8532 (p) REVERT: D 343 MET cc_start: 0.9137 (mpp) cc_final: 0.8772 (mmt) REVERT: D 588 MET cc_start: 0.7613 (mmm) cc_final: 0.7345 (mmm) REVERT: D 710 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.6889 (pmm150) REVERT: E 165 ARG cc_start: 0.9439 (tpp80) cc_final: 0.9123 (tmt170) outliers start: 25 outliers final: 5 residues processed: 145 average time/residue: 0.5046 time to fit residues: 82.5220 Evaluate side-chains 131 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 137 optimal weight: 0.6980 chunk 73 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 49 optimal weight: 50.0000 chunk 127 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.138241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.070253 restraints weight = 45143.348| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.84 r_work: 0.2973 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 362 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 383 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3382 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= 0.148 Angle : 0.715 20.712 20052 Z= 0.329 Chirality : 0.043 0.336 2188 Planarity : 0.004 0.040 2418 Dihedral : 13.368 177.455 2644 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.14 % Allowed : 18.47 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.21), residues: 1682 helix: 2.01 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -0.80 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 97 TYR 0.021 0.001 TYR D 261 PHE 0.018 0.001 PHE D 200 TRP 0.054 0.001 TRP C 25 HIS 0.003 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (14960) covalent geometry : angle 0.70956 / 0.33 (20030) SS BOND : bond 0.00206 / 0.10 ( 2) SS BOND : angle 0.47642 / 0.25 ( 4) hydrogen bonds : bond 0.04007 / 2.71 ( 924) hydrogen bonds : angle 4.13829 / 3.01 ( 2748) Misc. bond : bond 0.00086 / 0.04 ( 5) link_BETA1-3 : bond 0.00178 / 0.09 ( 1) link_BETA1-3 : angle 1.08206 / 0.56 ( 3) link_BETA1-4 : bond 0.00735 / 0.39 ( 1) link_BETA1-4 : angle 2.49898 / 1.31 ( 3) link_NAG-ASN : bond 0.00260 / 0.14 ( 4) link_NAG-ASN : angle 3.41055 / 1.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.492 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 202 MET cc_start: 0.4356 (OUTLIER) cc_final: 0.3893 (pmt) REVERT: A 233 MET cc_start: 0.3180 (mmt) cc_final: 0.2815 (mtm) REVERT: A 382 MET cc_start: 0.3368 (OUTLIER) cc_final: 0.3095 (ppp) REVERT: A 609 MET cc_start: 0.5792 (ppp) cc_final: 0.5191 (ppp) REVERT: B 58 MET cc_start: -0.0665 (mmp) cc_final: -0.1573 (mtp) REVERT: B 115 MET cc_start: 0.3759 (mmm) cc_final: 0.3310 (pmm) REVERT: B 172 LEU cc_start: 0.2999 (OUTLIER) cc_final: 0.2665 (mt) REVERT: C 46 MET cc_start: 0.5802 (ptt) cc_final: 0.4505 (pp-130) REVERT: D 114 MET cc_start: 0.9483 (tpt) cc_final: 0.9260 (tpt) REVERT: D 195 ASN cc_start: 0.9632 (OUTLIER) cc_final: 0.9031 (t0) REVERT: D 204 MET cc_start: 0.9362 (tpt) cc_final: 0.9082 (tpt) REVERT: D 268 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8528 (p) REVERT: D 343 MET cc_start: 0.9174 (mpp) cc_final: 0.8817 (mmt) REVERT: D 588 MET cc_start: 0.7566 (mmm) cc_final: 0.7352 (mmm) REVERT: D 710 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.6915 (pmm150) REVERT: F 26 MET cc_start: 0.8834 (pmm) cc_final: 0.8195 (pmm) outliers start: 17 outliers final: 9 residues processed: 143 average time/residue: 0.4872 time to fit residues: 78.5847 Evaluate side-chains 140 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 141 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 50.0000 chunk 32 optimal weight: 40.0000 chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.138306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.070290 restraints weight = 45013.743| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.01 r_work: 0.2972 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 383 | |-----------------------------------------------------------------------------| |-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: 423 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 14973 Z= 0.147 Angle : 0.723 21.094 20052 Z= 0.335 Chirality : 0.044 0.314 2188 Planarity : 0.004 0.042 2418 Dihedral : 13.298 177.740 2644 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.27 % Allowed : 18.81 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.21), residues: 1682 helix: 2.00 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 350 TYR 0.020 0.001 TYR D 261 PHE 0.015 0.001 PHE D 714 TRP 0.061 0.001 TRP C 25 HIS 0.003 0.000 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14960) covalent geometry : angle 0.71819 / 0.33 (20030) SS BOND : bond 0.00218 / 0.11 ( 2) SS BOND : angle 0.47675 / 0.26 ( 4) hydrogen bonds : bond 0.04009 / 2.71 ( 924) hydrogen bonds : angle 4.20285 / 3.07 ( 2748) Misc. bond : bond 0.00085 / 0.04 ( 5) link_BETA1-3 : bond 0.00333 / 0.18 ( 1) link_BETA1-3 : angle 1.13982 / 0.59 ( 3) link_BETA1-4 : bond 0.00814 / 0.43 ( 1) link_BETA1-4 : angle 2.47000 / 1.29 ( 3) link_NAG-ASN : bond 0.00271 / 0.14 ( 4) link_NAG-ASN : angle 3.35432 / 1.73 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.573 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 202 MET cc_start: 0.4318 (OUTLIER) cc_final: 0.3827 (pmt) REVERT: A 233 MET cc_start: 0.3123 (mmt) cc_final: 0.2726 (mtm) REVERT: A 382 MET cc_start: 0.3408 (OUTLIER) cc_final: 0.3104 (ppp) REVERT: A 609 MET cc_start: 0.5782 (ppp) cc_final: 0.5128 (ppp) REVERT: B 58 MET cc_start: -0.0502 (mmp) cc_final: -0.1440 (mtp) REVERT: B 115 MET cc_start: 0.3821 (mmm) cc_final: 0.3328 (pmm) REVERT: B 172 LEU cc_start: 0.2822 (OUTLIER) cc_final: 0.2479 (mt) REVERT: C 46 MET cc_start: 0.5789 (ptt) cc_final: 0.4368 (pp-130) REVERT: D 114 MET cc_start: 0.9471 (tpt) cc_final: 0.9257 (tpt) REVERT: D 195 ASN cc_start: 0.9618 (OUTLIER) cc_final: 0.9031 (t0) REVERT: D 204 MET cc_start: 0.9383 (tpt) cc_final: 0.9092 (tpt) REVERT: D 268 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8529 (p) REVERT: D 270 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (m-10) REVERT: D 284 PHE cc_start: 0.9306 (m-80) cc_final: 0.8974 (m-80) REVERT: D 343 MET cc_start: 0.9172 (mpp) cc_final: 0.8811 (mmt) REVERT: D 588 MET cc_start: 0.7461 (mmm) cc_final: 0.7250 (mmm) REVERT: D 602 GLU cc_start: 0.9182 (mp0) cc_final: 0.8945 (mp0) REVERT: F 26 MET cc_start: 0.8832 (pmm) cc_final: 0.8171 (pmm) outliers start: 19 outliers final: 12 residues processed: 144 average time/residue: 0.4244 time to fit residues: 69.3125 Evaluate side-chains 137 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 382 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 34 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 PHE Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 35 optimal weight: 30.0000 chunk 127 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 13 optimal weight: 0.0470 chunk 83 optimal weight: 10.0000 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.137489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070900 restraints weight = 44461.526| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.75 r_work: 0.2977 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 423 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 449 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14973 Z= 0.144 Angle : 0.735 20.692 20052 Z= 0.340 Chirality : 0.044 0.313 2188 Planarity : 0.004 0.041 2418 Dihedral : 13.242 178.235 2644 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.20 % Allowed : 19.08 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.21), residues: 1682 helix: 1.96 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -0.82 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 97 TYR 0.019 0.001 TYR D 261 PHE 0.015 0.001 PHE A 732 TRP 0.064 0.001 TRP C 25 HIS 0.003 0.000 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (14960) covalent geometry : angle 0.73014 / 0.34 (20030) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 0.47401 / 0.25 ( 4) hydrogen bonds : bond 0.04034 / 2.72 ( 924) hydrogen bonds : angle 4.23483 / 3.08 ( 2748) Misc. bond : bond 0.00083 / 0.04 ( 5) link_BETA1-3 : bond 0.00465 / 0.24 ( 1) link_BETA1-3 : angle 1.19033 / 0.62 ( 3) link_BETA1-4 : bond 0.00557 / 0.29 ( 1) link_BETA1-4 : angle 2.48097 / 1.30 ( 3) link_NAG-ASN : bond 0.00264 / 0.14 ( 4) link_NAG-ASN : angle 3.31226 / 1.70 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7545.03 seconds wall clock time: 128 minutes 47.01 seconds (7727.01 seconds total)