Starting phenix.real_space_refine on Sun Jul 5 21:36:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pet_17636/07_2026/8pet_17636_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pet_17636/07_2026/8pet_17636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pet_17636/07_2026/8pet_17636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pet_17636/07_2026/8pet_17636.map" model { file = "/net/cci-nas-00/data/ceres_data/8pet_17636/07_2026/8pet_17636_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pet_17636/07_2026/8pet_17636_trim.cif" } resolution = 2.6 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= 0.006 sd= 0.077 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 S 84 5.16 5 C 10022 2.51 5 N 2446 2.21 5 O 2892 1.98 5 H 14629 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 30080 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 5569 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 5536 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 343, 5536 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 bond proxies already assigned to first conformer: 5572 Chain: "B" Number of atoms: 5489 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 332, 5432 Classifications: {'peptide': 332} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 332, 5432 Classifications: {'peptide': 332} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 bond proxies already assigned to first conformer: 5440 Chain: "D" Number of atoms: 5459 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 5411 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 330, 5411 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 bond proxies already assigned to first conformer: 5429 Chain: "C" Number of atoms: 5569 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 5536 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 343, 5536 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 bond proxies already assigned to first conformer: 5572 Chain: "E" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5417 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "F" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1857 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PIO': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 41 Unusual residues: {' ZN': 1, 'D10': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 50 Unusual residues: {'D10': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PIO': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'D10': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.55, per 1000 atoms: 0.25 Number of scatterers: 30080 At special positions: 0 Unit cell: (120.064, 92.288, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 84 16.00 P 6 15.00 O 2892 8.00 N 2446 7.00 C 10022 6.00 H 14629 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 153 " distance=2.04 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN D 80 " " NAG I 1 " - " ASN E 80 " " NAG a 1 " - " ASN A 111 " " NAG b 1 " - " ASN B 149 " " NAG c 1 " - " ASN D 149 " " NAG d 1 " - " ASN C 111 " " NAG e 1 " - " ASN E 149 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 505 " pdb="ZN ZN B 505 " - pdb=" ND1 HIS E 267 " pdb="ZN ZN B 505 " - pdb=" NE2 HIS D 267 " pdb="ZN ZN B 505 " - pdb=" NE2 HIS B 267 " 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 18 sheets defined 39.2% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.618A pdb=" N LEU A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 223 through 230 removed outlier: 3.525A pdb=" N ILE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 251 through 277 Processing helix chain 'A' and resid 284 through 309 removed outlier: 3.603A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 416 removed outlier: 4.118A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.502A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.874A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.660A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 472 removed outlier: 3.672A pdb=" N ASP B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Proline residue: B 457 - end of helix Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.692A pdb=" N LEU D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 237 removed outlier: 3.709A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 246 through 272 removed outlier: 3.683A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 308 Processing helix chain 'D' and resid 445 through 472 removed outlier: 3.573A pdb=" N ASP D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) Proline residue: D 457 - end of helix Processing helix chain 'C' and resid 13 through 23 removed outlier: 3.967A pdb=" N LEU C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 76 Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 142 through 146 removed outlier: 4.505A pdb=" N ASP C 145 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.791A pdb=" N SER C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 251 through 277 removed outlier: 3.530A pdb=" N ASN C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 310 removed outlier: 3.635A pdb=" N PHE C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 416 removed outlier: 3.903A pdb=" N ILE C 398 " --> pdb=" O ARG C 394 " (cutoff:3.500A) Proline residue: C 401 - end of helix Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.572A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.590A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.685A pdb=" N SER E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 267 removed outlier: 3.591A pdb=" N HIS E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.722A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 472 removed outlier: 3.890A pdb=" N ASP E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 454 " --> pdb=" O ARG E 450 " (cutoff:3.500A) Proline residue: E 457 - end of helix Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 108 through 112 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.921A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP A 63 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE A 50 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N PHE A 65 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 48 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ARG A 67 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE A 46 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER A 69 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASP A 44 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LYS A 71 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N LYS A 42 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.908A pdb=" N ASP A 63 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE A 50 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N PHE A 65 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 48 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ARG A 67 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE A 46 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER A 69 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASP A 44 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LYS A 71 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N LYS A 42 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.360A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.388A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.551A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.069A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.696A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.457A pdb=" N ASP D 101 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA D 135 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.934A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 83 through 86 removed outlier: 4.641A pdb=" N LEU C 119 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU C 59 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR C 61 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 63 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS C 71 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU C 40 " --> pdb=" O LYS C 71 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR C 39 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU C 170 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL C 41 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 104 through 109 removed outlier: 6.955A pdb=" N ARG C 136 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER C 107 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR C 134 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA C 109 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ARG C 132 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU C 59 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR C 61 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 63 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS C 71 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU C 40 " --> pdb=" O LYS C 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.376A pdb=" N SER C 159 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 211 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY C 195 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS C 220 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU C 193 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.567A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.678A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.782A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.511A pdb=" N ILE F 33 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.592A pdb=" N TYR F 114 " --> pdb=" O ALA F 98 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2384 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: 7.19 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14620 1.03 - 1.23: 101 1.23 - 1.42: 6618 1.42 - 1.62: 8897 1.62 - 1.82: 146 Bond restraints: 30382 Sorted by residual: bond pdb=" O4 PIO A 502 " pdb=" P4 PIO A 502 " ideal model delta sigma weight residual 1.710 1.587 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" O4 PIO C 502 " pdb=" P4 PIO C 502 " ideal model delta sigma weight residual 1.710 1.590 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" O5 PIO A 502 " pdb=" P5 PIO A 502 " ideal model delta sigma weight residual 1.699 1.604 0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" O5 PIO C 502 " pdb=" P5 PIO C 502 " ideal model delta sigma weight residual 1.699 1.605 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O13 PIO A 502 " pdb=" P1 PIO A 502 " ideal model delta sigma weight residual 1.651 1.583 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 30377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 53970 2.00 - 4.01: 338 4.01 - 6.01: 37 6.01 - 8.01: 3 8.01 - 10.02: 2 Bond angle restraints: 54350 Sorted by residual: angle pdb=" C4 PIO C 502 " pdb=" O4 PIO C 502 " pdb=" P4 PIO C 502 " ideal model delta sigma weight residual 121.90 131.92 -10.02 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C4 PIO A 502 " pdb=" O4 PIO A 502 " pdb=" P4 PIO A 502 " ideal model delta sigma weight residual 121.90 131.28 -9.38 3.00e+00 1.11e-01 9.78e+00 angle pdb=" N ARG F 67 " pdb=" CA ARG F 67 " pdb=" C ARG F 67 " ideal model delta sigma weight residual 113.18 109.85 3.33 1.33e+00 5.65e-01 6.27e+00 angle pdb=" O1 PIO C 502 " pdb=" P1 PIO C 502 " pdb=" O13 PIO C 502 " ideal model delta sigma weight residual 97.64 104.72 -7.08 3.00e+00 1.11e-01 5.57e+00 angle pdb=" C MET A 112 " pdb=" N THR A 113 " pdb=" CA THR A 113 " ideal model delta sigma weight residual 121.70 125.89 -4.19 1.80e+00 3.09e-01 5.41e+00 ... (remaining 54345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 14288 21.18 - 42.37: 397 42.37 - 63.55: 131 63.55 - 84.73: 36 84.73 - 105.91: 21 Dihedral angle restraints: 14873 sinusoidal: 8202 harmonic: 6671 Sorted by residual: dihedral pdb=" CA PRO E 276 " pdb=" C PRO E 276 " pdb=" N TYR E 277 " pdb=" CA TYR E 277 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA VAL C 64 " pdb=" C VAL C 64 " pdb=" N PHE C 65 " pdb=" CA PHE C 65 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA VAL A 64 " pdb=" C VAL A 64 " pdb=" N PHE A 65 " pdb=" CA PHE A 65 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 14870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2011 0.050 - 0.100: 336 0.100 - 0.150: 116 0.150 - 0.200: 5 0.200 - 0.250: 7 Chirality restraints: 2475 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN C 111 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2472 not shown) Planarity restraints: 4300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " -0.024 2.00e-02 2.50e+03 1.99e-02 4.93e+00 pdb=" C7 NAG c 2 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " 0.032 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " -0.024 2.00e-02 2.50e+03 1.98e-02 4.92e+00 pdb=" C7 NAG b 1 " 0.007 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " 0.031 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.023 2.00e-02 2.50e+03 1.90e-02 4.52e+00 pdb=" C7 NAG a 2 " 0.007 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.030 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.004 2.00e-02 2.50e+03 ... (remaining 4297 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1886 2.22 - 2.81: 63018 2.81 - 3.41: 80681 3.41 - 4.00: 114514 4.00 - 4.60: 174135 Nonbonded interactions: 434234 Sorted by model distance: nonbonded pdb=" OD1 ASP C 55 " pdb=" HH TYR C 191 " model vdw 1.621 2.450 nonbonded pdb=" HZ1 LYS C 312 " pdb=" O41 PIO C 502 " model vdw 1.622 2.450 nonbonded pdb=" OD1 ASP A 55 " pdb=" HH TYR A 191 " model vdw 1.631 2.450 nonbonded pdb=" OE1 GLU B 155 " pdb=" HE ARG B 207 " model vdw 1.633 2.450 nonbonded pdb=" OD2 ASP E 95 " pdb=" H GLY E 158 " model vdw 1.639 2.450 ... (remaining 434229 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 12 through 66 or resid 68 through 394 or resid 396 through \ 502)) selection = (chain 'C' and (resid 12 through 66 or resid 68 through 394 or resid 396 through \ 502)) } ncs_group { reference = (chain 'B' and (resid 9 through 296 or resid 298 through 300 or resid 302 throug \ h 309 or resid 444 through 445 or resid 447 through 450 or resid 452 through 503 \ )) selection = (chain 'D' and (resid 9 through 296 or resid 298 through 300 or resid 302 throug \ h 445 or resid 447 through 450 or resid 452 through 503)) selection = (chain 'E' and (resid 9 through 296 or resid 298 through 300 or resid 302 throug \ h 445 or resid 447 through 450 or resid 452 through 503)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.200 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.880 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 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 0.123 15792 Z= 0.242 Angle : 0.587 10.016 21473 Z= 0.271 Chirality : 0.044 0.250 2475 Planarity : 0.004 0.040 2580 Dihedral : 12.667 105.913 6203 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.74 % Allowed : 2.86 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1791 helix: 0.65 (0.21), residues: 590 sheet: 0.55 (0.23), residues: 506 loop : 0.31 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 274 TYR 0.016 0.002 TYR D 299 PHE 0.011 0.001 PHE E 98 TRP 0.007 0.001 TRP A 412 HIS 0.004 0.001 HIS D 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (15752) covalent geometry : angle 0.57711 / 0.27 (21368) SS BOND : bond 0.00370 / 0.18 ( 6) SS BOND : angle 1.18664 / 0.68 ( 12) hydrogen bonds : bond 0.20442 / 13.69 ( 753) hydrogen bonds : angle 7.53449 / 5.30 ( 2384) metal coordination : bond 0.00245 / 0.10 ( 3) link_ALPHA1-3 : bond 0.00276 / 0.14 ( 5) link_ALPHA1-3 : angle 1.16370 / 0.66 ( 15) link_ALPHA1-6 : bond 0.00426 / 0.27 ( 5) link_ALPHA1-6 : angle 1.04810 / 0.60 ( 15) link_BETA1-4 : bond 0.00520 / 0.36 ( 13) link_BETA1-4 : angle 1.91134 / 1.23 ( 39) link_NAG-ASN : bond 0.00184 / 0.10 ( 8) link_NAG-ASN : angle 1.83105 / 1.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 311 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7311 (mtt-85) REVERT: A 204 GLN cc_start: 0.8197 (mt0) cc_final: 0.7915 (tp-100) REVERT: A 209 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8293 (mt-10) REVERT: A 277 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7796 (mt) REVERT: B 49 MET cc_start: 0.7935 (mtp) cc_final: 0.7406 (pp-130) REVERT: B 68 ARG cc_start: 0.8415 (ttt-90) cc_final: 0.8145 (tpp80) REVERT: B 103 LYS cc_start: 0.8389 (tptt) cc_final: 0.8063 (tptp) REVERT: B 137 MET cc_start: 0.7934 (tpt) cc_final: 0.7724 (tpt) REVERT: B 165 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8431 (mt-10) REVERT: B 173 LYS cc_start: 0.8607 (mttm) cc_final: 0.8368 (mtpp) REVERT: B 215 LYS cc_start: 0.8640 (tttt) cc_final: 0.8083 (tptp) REVERT: B 450 ARG cc_start: 0.8249 (ttt180) cc_final: 0.7922 (mtm110) REVERT: B 454 ILE cc_start: 0.9077 (mt) cc_final: 0.8847 (mm) REVERT: D 64 GLN cc_start: 0.8685 (mt0) cc_final: 0.8481 (mp10) REVERT: D 103 LYS cc_start: 0.8566 (tptt) cc_final: 0.8208 (ttpp) REVERT: D 137 MET cc_start: 0.7960 (tpt) cc_final: 0.7609 (mmm) REVERT: D 165 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8204 (mm-30) REVERT: D 215 LYS cc_start: 0.8523 (tttt) cc_final: 0.8292 (tptp) REVERT: D 227 MET cc_start: 0.8886 (ttt) cc_final: 0.8653 (ttt) REVERT: C 123 GLU cc_start: 0.8306 (pt0) cc_final: 0.7780 (pm20) REVERT: C 144 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7930 (mp0) REVERT: C 170 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7890 (mt-10) REVERT: C 190 GLN cc_start: 0.7906 (pt0) cc_final: 0.7640 (pm20) REVERT: E 147 GLU cc_start: 0.8145 (tt0) cc_final: 0.7931 (tt0) REVERT: E 215 LYS cc_start: 0.8869 (tttt) cc_final: 0.8505 (tptt) REVERT: E 218 ILE cc_start: 0.8431 (tp) cc_final: 0.8221 (mt) REVERT: E 224 GLN cc_start: 0.8481 (tp40) cc_final: 0.7750 (mm-40) REVERT: E 235 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8911 (mp) REVERT: E 462 LEU cc_start: 0.8709 (tp) cc_final: 0.8423 (tp) REVERT: F 46 GLU cc_start: 0.8615 (tt0) cc_final: 0.8357 (tm-30) REVERT: F 73 ASP cc_start: 0.6442 (t0) cc_final: 0.6125 (t0) REVERT: F 82 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7606 (mp0) outliers start: 11 outliers final: 1 residues processed: 320 average time/residue: 1.4186 time to fit residues: 497.5732 Evaluate side-chains 237 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 234 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 189 ASN A 408 ASN B 41 ASN B 64 GLN D 265 ASN C 408 ASN F 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.082748 restraints weight = 78027.683| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.32 r_work: 0.2745 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15792 Z= 0.189 Angle : 0.582 6.018 21473 Z= 0.309 Chirality : 0.044 0.178 2475 Planarity : 0.005 0.077 2580 Dihedral : 11.042 83.639 2809 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.99 % Allowed : 9.25 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1791 helix: 1.31 (0.20), residues: 594 sheet: 0.48 (0.23), residues: 480 loop : 0.11 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 85 TYR 0.021 0.002 TYR B 299 PHE 0.020 0.002 PHE A 15 TRP 0.007 0.001 TRP E 451 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (15752) covalent geometry : angle 0.56815 / 0.31 (21368) SS BOND : bond 0.00456 / 0.21 ( 6) SS BOND : angle 1.02539 / 0.60 ( 12) hydrogen bonds : bond 0.05858 / 4.00 ( 753) hydrogen bonds : angle 5.33711 / 3.76 ( 2384) metal coordination : bond 0.00268 / 0.13 ( 3) link_ALPHA1-3 : bond 0.00715 / 0.36 ( 5) link_ALPHA1-3 : angle 2.53965 / 1.57 ( 15) link_ALPHA1-6 : bond 0.00477 / 0.29 ( 5) link_ALPHA1-6 : angle 1.98465 / 1.19 ( 15) link_BETA1-4 : bond 0.00450 / 0.28 ( 13) link_BETA1-4 : angle 1.89932 / 1.28 ( 39) link_NAG-ASN : bond 0.00181 / 0.10 ( 8) link_NAG-ASN : angle 1.73101 / 1.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7787 (ptp90) REVERT: A 120 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7307 (mtt-85) REVERT: A 277 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7727 (mt) REVERT: B 49 MET cc_start: 0.8107 (mtp) cc_final: 0.7598 (pp-130) REVERT: B 215 LYS cc_start: 0.8814 (tttt) cc_final: 0.8452 (tptp) REVERT: D 40 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8788 (mtt) REVERT: D 224 GLN cc_start: 0.8695 (mm110) cc_final: 0.8456 (mp10) REVERT: D 268 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8482 (mp) REVERT: D 286 MET cc_start: 0.8577 (tpt) cc_final: 0.8265 (tpt) REVERT: C 277 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6532 (mt) REVERT: E 18 LYS cc_start: 0.8213 (pttp) cc_final: 0.7749 (ptpt) REVERT: E 215 LYS cc_start: 0.8932 (tttt) cc_final: 0.8702 (tptt) REVERT: E 235 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9016 (mp) REVERT: E 462 LEU cc_start: 0.8786 (tp) cc_final: 0.8530 (tp) REVERT: F 46 GLU cc_start: 0.8640 (tt0) cc_final: 0.8236 (tm-30) REVERT: F 73 ASP cc_start: 0.6225 (t0) cc_final: 0.5897 (t0) REVERT: F 82 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7480 (mp0) outliers start: 16 outliers final: 1 residues processed: 236 average time/residue: 1.3798 time to fit residues: 356.9340 Evaluate side-chains 217 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN D 265 ASN F 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.082685 restraints weight = 81231.923| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.45 r_work: 0.2746 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15792 Z= 0.198 Angle : 0.576 5.922 21473 Z= 0.301 Chirality : 0.044 0.215 2475 Planarity : 0.005 0.071 2580 Dihedral : 10.439 83.399 2808 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.30 % Allowed : 10.92 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1791 helix: 1.44 (0.20), residues: 593 sheet: 0.47 (0.23), residues: 480 loop : 0.05 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 180 TYR 0.022 0.002 TYR D 299 PHE 0.014 0.002 PHE A 304 TRP 0.006 0.001 TRP A 412 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (15752) covalent geometry : angle 0.56279 / 0.30 (21368) SS BOND : bond 0.00487 / 0.23 ( 6) SS BOND : angle 1.19119 / 0.70 ( 12) hydrogen bonds : bond 0.05004 / 3.44 ( 753) hydrogen bonds : angle 4.97990 / 3.51 ( 2384) metal coordination : bond 0.00237 / 0.09 ( 3) link_ALPHA1-3 : bond 0.00962 / 0.48 ( 5) link_ALPHA1-3 : angle 2.10866 / 1.32 ( 15) link_ALPHA1-6 : bond 0.00644 / 0.37 ( 5) link_ALPHA1-6 : angle 1.91822 / 1.16 ( 15) link_BETA1-4 : bond 0.00450 / 0.29 ( 13) link_BETA1-4 : angle 1.82430 / 1.20 ( 39) link_NAG-ASN : bond 0.00200 / 0.11 ( 8) link_NAG-ASN : angle 1.78276 / 1.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7741 (ptp90) REVERT: A 120 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7275 (mtt-85) REVERT: A 170 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: A 277 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7858 (mp) REVERT: B 18 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8176 (ttmm) REVERT: B 49 MET cc_start: 0.8065 (mtp) cc_final: 0.7557 (pp-130) REVERT: B 103 LYS cc_start: 0.8618 (tptt) cc_final: 0.8308 (tptp) REVERT: B 215 LYS cc_start: 0.8818 (tttt) cc_final: 0.8381 (tptp) REVERT: D 40 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8792 (mtt) REVERT: D 224 GLN cc_start: 0.8693 (mm110) cc_final: 0.8474 (mp10) REVERT: D 286 MET cc_start: 0.8600 (tpt) cc_final: 0.8246 (tpt) REVERT: C 183 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: C 277 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6570 (mt) REVERT: E 215 LYS cc_start: 0.8936 (tttt) cc_final: 0.8675 (tptt) REVERT: E 235 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8994 (mp) REVERT: E 462 LEU cc_start: 0.8777 (tp) cc_final: 0.8520 (tp) REVERT: F 46 GLU cc_start: 0.8669 (tt0) cc_final: 0.8272 (tm-30) REVERT: F 73 ASP cc_start: 0.6234 (t0) cc_final: 0.5889 (t0) REVERT: F 82 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7481 (mp0) outliers start: 21 outliers final: 8 residues processed: 230 average time/residue: 1.4342 time to fit residues: 362.2678 Evaluate side-chains 222 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 85 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 89 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 64 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.084017 restraints weight = 82227.119| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.40 r_work: 0.2772 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15792 Z= 0.118 Angle : 0.529 6.036 21473 Z= 0.275 Chirality : 0.043 0.223 2475 Planarity : 0.004 0.058 2580 Dihedral : 9.580 83.792 2808 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.46 % Favored : 98.48 % Rotamer: Outliers : 0.87 % Allowed : 12.10 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % 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: 1.06 (0.20), residues: 1791 helix: 1.67 (0.20), residues: 595 sheet: 0.50 (0.24), residues: 464 loop : 0.15 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 85 TYR 0.024 0.001 TYR D 299 PHE 0.016 0.001 PHE A 304 TRP 0.006 0.001 TRP C 70 HIS 0.003 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15752) covalent geometry : angle 0.51796 / 0.27 (21368) SS BOND : bond 0.00276 / 0.13 ( 6) SS BOND : angle 0.83159 / 0.50 ( 12) hydrogen bonds : bond 0.04111 / 2.81 ( 753) hydrogen bonds : angle 4.68182 / 3.30 ( 2384) metal coordination : bond 0.00081 / 0.04 ( 3) link_ALPHA1-3 : bond 0.01062 / 0.55 ( 5) link_ALPHA1-3 : angle 2.11809 / 1.31 ( 15) link_ALPHA1-6 : bond 0.00825 / 0.46 ( 5) link_ALPHA1-6 : angle 1.89009 / 1.12 ( 15) link_BETA1-4 : bond 0.00365 / 0.21 ( 13) link_BETA1-4 : angle 1.56562 / 1.04 ( 39) link_NAG-ASN : bond 0.00183 / 0.10 ( 8) link_NAG-ASN : angle 1.46485 / 0.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7239 (mtt-85) REVERT: A 170 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 277 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8024 (mt) REVERT: B 18 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8187 (ttmm) REVERT: B 49 MET cc_start: 0.8131 (mtp) cc_final: 0.7582 (pp-130) REVERT: B 215 LYS cc_start: 0.8834 (tttt) cc_final: 0.8398 (tptp) REVERT: D 40 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8724 (mtt) REVERT: D 224 GLN cc_start: 0.8667 (mm110) cc_final: 0.8439 (mp10) REVERT: C 277 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6558 (mt) REVERT: E 215 LYS cc_start: 0.8930 (tttt) cc_final: 0.8663 (tptt) REVERT: E 462 LEU cc_start: 0.8742 (tp) cc_final: 0.8471 (tp) REVERT: F 46 GLU cc_start: 0.8667 (tt0) cc_final: 0.8285 (tm-30) REVERT: F 73 ASP cc_start: 0.6240 (t0) cc_final: 0.5899 (t0) REVERT: F 82 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7503 (mp0) outliers start: 14 outliers final: 3 residues processed: 222 average time/residue: 1.3913 time to fit residues: 338.3673 Evaluate side-chains 209 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 100 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.083310 restraints weight = 80431.456| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.38 r_work: 0.2759 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15792 Z= 0.160 Angle : 0.543 6.122 21473 Z= 0.281 Chirality : 0.043 0.211 2475 Planarity : 0.004 0.059 2580 Dihedral : 9.299 84.352 2808 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.24 % Allowed : 11.73 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % 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: 1.06 (0.19), residues: 1791 helix: 1.70 (0.20), residues: 595 sheet: 0.48 (0.23), residues: 468 loop : 0.15 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 85 TYR 0.024 0.002 TYR D 299 PHE 0.016 0.001 PHE A 304 TRP 0.006 0.001 TRP C 70 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15752) covalent geometry : angle 0.53039 / 0.28 (21368) SS BOND : bond 0.00417 / 0.19 ( 6) SS BOND : angle 1.06350 / 0.63 ( 12) hydrogen bonds : bond 0.04186 / 2.88 ( 753) hydrogen bonds : angle 4.62176 / 3.26 ( 2384) metal coordination : bond 0.00302 / 0.12 ( 3) link_ALPHA1-3 : bond 0.00970 / 0.50 ( 5) link_ALPHA1-3 : angle 2.17527 / 1.36 ( 15) link_ALPHA1-6 : bond 0.00815 / 0.45 ( 5) link_ALPHA1-6 : angle 1.73282 / 1.01 ( 15) link_BETA1-4 : bond 0.00439 / 0.27 ( 13) link_BETA1-4 : angle 1.71208 / 1.13 ( 39) link_NAG-ASN : bond 0.00186 / 0.10 ( 8) link_NAG-ASN : angle 1.65379 / 1.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7001 (mttt) REVERT: A 120 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7237 (mtt-85) REVERT: A 170 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: B 18 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8195 (ttmm) REVERT: B 49 MET cc_start: 0.8081 (mtp) cc_final: 0.7589 (pp-130) REVERT: B 215 LYS cc_start: 0.8818 (tttt) cc_final: 0.8384 (tptp) REVERT: D 13 LYS cc_start: 0.8047 (tttp) cc_final: 0.7774 (tttt) REVERT: D 40 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8715 (mtt) REVERT: D 224 GLN cc_start: 0.8669 (mm110) cc_final: 0.8442 (mp10) REVERT: D 227 MET cc_start: 0.8584 (ttt) cc_final: 0.8356 (ttt) REVERT: C 277 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6561 (mt) REVERT: E 215 LYS cc_start: 0.8922 (tttt) cc_final: 0.8665 (tptt) REVERT: E 235 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9014 (mp) REVERT: F 46 GLU cc_start: 0.8705 (tt0) cc_final: 0.8328 (tm-30) REVERT: F 73 ASP cc_start: 0.6276 (t0) cc_final: 0.5921 (t0) REVERT: F 82 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7526 (mp0) outliers start: 20 outliers final: 8 residues processed: 219 average time/residue: 1.4149 time to fit residues: 338.8894 Evaluate side-chains 214 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 74 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN D 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.083332 restraints weight = 77040.054| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.35 r_work: 0.2772 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15792 Z= 0.145 Angle : 0.532 6.114 21473 Z= 0.275 Chirality : 0.043 0.218 2475 Planarity : 0.004 0.063 2580 Dihedral : 8.793 86.246 2808 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.06 % Allowed : 12.41 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % 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: 1.11 (0.20), residues: 1791 helix: 1.79 (0.20), residues: 594 sheet: 0.46 (0.23), residues: 476 loop : 0.16 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 85 TYR 0.025 0.002 TYR D 299 PHE 0.017 0.001 PHE A 304 TRP 0.006 0.001 TRP C 70 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (15752) covalent geometry : angle 0.51950 / 0.27 (21368) SS BOND : bond 0.00348 / 0.16 ( 6) SS BOND : angle 0.97287 / 0.58 ( 12) hydrogen bonds : bond 0.04014 / 2.76 ( 753) hydrogen bonds : angle 4.53364 / 3.20 ( 2384) metal coordination : bond 0.00131 / 0.05 ( 3) link_ALPHA1-3 : bond 0.00993 / 0.51 ( 5) link_ALPHA1-3 : angle 2.06765 / 1.28 ( 15) link_ALPHA1-6 : bond 0.01005 / 0.55 ( 5) link_ALPHA1-6 : angle 2.20728 / 1.43 ( 15) link_BETA1-4 : bond 0.00430 / 0.26 ( 13) link_BETA1-4 : angle 1.66582 / 1.10 ( 39) link_NAG-ASN : bond 0.00193 / 0.11 ( 8) link_NAG-ASN : angle 1.58626 / 1.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8074 (ttm170) cc_final: 0.7655 (ptp90) REVERT: A 78 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7070 (mttt) REVERT: A 120 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7192 (mtt-85) REVERT: A 170 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: B 18 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8199 (ttmm) REVERT: B 49 MET cc_start: 0.8061 (mtp) cc_final: 0.7572 (pp-130) REVERT: B 215 LYS cc_start: 0.8804 (tttt) cc_final: 0.8359 (tptp) REVERT: D 13 LYS cc_start: 0.8057 (tttp) cc_final: 0.7790 (tttt) REVERT: D 40 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8695 (mtt) REVERT: D 224 GLN cc_start: 0.8648 (mm110) cc_final: 0.8415 (mp10) REVERT: D 227 MET cc_start: 0.8571 (ttt) cc_final: 0.8340 (ttt) REVERT: D 286 MET cc_start: 0.8548 (tpt) cc_final: 0.8224 (tpt) REVERT: C 277 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6542 (mt) REVERT: E 215 LYS cc_start: 0.8903 (tttt) cc_final: 0.8634 (tptt) REVERT: E 462 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8610 (tp) REVERT: F 46 GLU cc_start: 0.8665 (tt0) cc_final: 0.8308 (tm-30) REVERT: F 73 ASP cc_start: 0.6273 (t0) cc_final: 0.5881 (t0) REVERT: F 82 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7506 (mp0) outliers start: 16 outliers final: 7 residues processed: 214 average time/residue: 1.4235 time to fit residues: 332.7319 Evaluate side-chains 213 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 462 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN D 265 ASN F 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.082118 restraints weight = 84128.151| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.56 r_work: 0.2731 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15792 Z= 0.207 Angle : 0.567 6.165 21473 Z= 0.293 Chirality : 0.044 0.212 2475 Planarity : 0.004 0.061 2580 Dihedral : 9.067 89.250 2808 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 12.54 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % 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: 1.03 (0.19), residues: 1791 helix: 1.69 (0.20), residues: 594 sheet: 0.46 (0.23), residues: 476 loop : 0.10 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 85 TYR 0.024 0.002 TYR D 299 PHE 0.017 0.002 PHE A 304 TRP 0.006 0.001 TRP A 70 HIS 0.006 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (15752) covalent geometry : angle 0.55290 / 0.29 (21368) SS BOND : bond 0.00532 / 0.25 ( 6) SS BOND : angle 1.27094 / 0.75 ( 12) hydrogen bonds : bond 0.04353 / 3.00 ( 753) hydrogen bonds : angle 4.62165 / 3.26 ( 2384) metal coordination : bond 0.00355 / 0.14 ( 3) link_ALPHA1-3 : bond 0.00903 / 0.46 ( 5) link_ALPHA1-3 : angle 2.22805 / 1.38 ( 15) link_ALPHA1-6 : bond 0.00783 / 0.44 ( 5) link_ALPHA1-6 : angle 1.82958 / 1.12 ( 15) link_BETA1-4 : bond 0.00506 / 0.32 ( 13) link_BETA1-4 : angle 1.86887 / 1.23 ( 39) link_NAG-ASN : bond 0.00216 / 0.12 ( 8) link_NAG-ASN : angle 1.84645 / 1.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8111 (ttm170) cc_final: 0.7694 (ptp90) REVERT: A 78 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7119 (mttt) REVERT: A 120 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7324 (mtt-85) REVERT: A 170 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: B 18 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8182 (ttmm) REVERT: B 49 MET cc_start: 0.8130 (mtp) cc_final: 0.7497 (pp-130) REVERT: B 215 LYS cc_start: 0.8832 (tttt) cc_final: 0.8403 (tptp) REVERT: B 268 LEU cc_start: 0.8931 (tt) cc_final: 0.8716 (tp) REVERT: D 40 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8774 (mtt) REVERT: D 224 GLN cc_start: 0.8696 (mm110) cc_final: 0.8431 (mp10) REVERT: D 227 MET cc_start: 0.8625 (ttt) cc_final: 0.8411 (ttt) REVERT: D 286 MET cc_start: 0.8610 (tpt) cc_final: 0.8307 (tpt) REVERT: C 277 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6592 (mt) REVERT: E 215 LYS cc_start: 0.8945 (tttt) cc_final: 0.8685 (tptt) REVERT: E 235 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9034 (mp) REVERT: E 462 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8639 (tp) REVERT: F 46 GLU cc_start: 0.8746 (tt0) cc_final: 0.8392 (tm-30) REVERT: F 73 ASP cc_start: 0.6292 (t0) cc_final: 0.5910 (t0) REVERT: F 82 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7532 (mp0) outliers start: 18 outliers final: 9 residues processed: 215 average time/residue: 1.3887 time to fit residues: 327.4574 Evaluate side-chains 216 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 462 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 265 ASN D 265 ASN F 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.083892 restraints weight = 78601.224| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.34 r_work: 0.2771 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15792 Z= 0.128 Angle : 0.523 6.126 21473 Z= 0.271 Chirality : 0.042 0.222 2475 Planarity : 0.004 0.074 2580 Dihedral : 8.618 89.560 2808 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.12 % Allowed : 12.60 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % 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: 1.19 (0.20), residues: 1791 helix: 1.84 (0.20), residues: 595 sheet: 0.53 (0.24), residues: 469 loop : 0.20 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 85 TYR 0.025 0.001 TYR D 299 PHE 0.016 0.001 PHE A 304 TRP 0.006 0.001 TRP C 70 HIS 0.004 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15752) covalent geometry : angle 0.51174 / 0.27 (21368) SS BOND : bond 0.00294 / 0.14 ( 6) SS BOND : angle 0.89062 / 0.52 ( 12) hydrogen bonds : bond 0.03873 / 2.66 ( 753) hydrogen bonds : angle 4.47086 / 3.15 ( 2384) metal coordination : bond 0.00525 / 0.22 ( 3) link_ALPHA1-3 : bond 0.00951 / 0.49 ( 5) link_ALPHA1-3 : angle 1.95193 / 1.19 ( 15) link_ALPHA1-6 : bond 0.00860 / 0.48 ( 5) link_ALPHA1-6 : angle 1.86062 / 1.15 ( 15) link_BETA1-4 : bond 0.00407 / 0.24 ( 13) link_BETA1-4 : angle 1.62776 / 1.07 ( 39) link_NAG-ASN : bond 0.00202 / 0.12 ( 8) link_NAG-ASN : angle 1.54750 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7659 (ptp90) REVERT: A 78 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7119 (mttt) REVERT: A 120 ARG cc_start: 0.7548 (mtt180) cc_final: 0.7202 (mtt-85) REVERT: A 170 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: B 18 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8176 (ttmm) REVERT: B 49 MET cc_start: 0.8071 (mtp) cc_final: 0.7599 (pp-130) REVERT: B 215 LYS cc_start: 0.8811 (tttt) cc_final: 0.8376 (tptp) REVERT: B 268 LEU cc_start: 0.8896 (tt) cc_final: 0.8696 (tp) REVERT: D 40 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8669 (mtt) REVERT: D 224 GLN cc_start: 0.8651 (mm110) cc_final: 0.8395 (mp10) REVERT: D 227 MET cc_start: 0.8575 (ttt) cc_final: 0.8344 (ttt) REVERT: D 286 MET cc_start: 0.8531 (tpt) cc_final: 0.8246 (tpt) REVERT: C 277 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6570 (mt) REVERT: E 215 LYS cc_start: 0.8898 (tttt) cc_final: 0.8638 (tptt) REVERT: E 462 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8630 (tp) REVERT: F 46 GLU cc_start: 0.8685 (tt0) cc_final: 0.8323 (tm-30) REVERT: F 73 ASP cc_start: 0.6334 (t0) cc_final: 0.5939 (t0) REVERT: F 82 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7494 (mp0) outliers start: 17 outliers final: 7 residues processed: 215 average time/residue: 1.4303 time to fit residues: 336.4067 Evaluate side-chains 208 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 462 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 ASN D 265 ASN F 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.081912 restraints weight = 82259.463| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.53 r_work: 0.2730 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15792 Z= 0.216 Angle : 0.574 6.187 21473 Z= 0.297 Chirality : 0.044 0.212 2475 Planarity : 0.004 0.071 2580 Dihedral : 8.901 85.432 2808 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.12 % Allowed : 12.54 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % 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: 1.06 (0.20), residues: 1791 helix: 1.69 (0.20), residues: 595 sheet: 0.50 (0.23), residues: 473 loop : 0.13 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 85 TYR 0.024 0.002 TYR D 299 PHE 0.018 0.002 PHE A 304 TRP 0.006 0.001 TRP A 70 HIS 0.006 0.001 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (15752) covalent geometry : angle 0.56007 / 0.29 (21368) SS BOND : bond 0.00563 / 0.26 ( 6) SS BOND : angle 1.32275 / 0.78 ( 12) hydrogen bonds : bond 0.04344 / 3.00 ( 753) hydrogen bonds : angle 4.59819 / 3.24 ( 2384) metal coordination : bond 0.00411 / 0.21 ( 3) link_ALPHA1-3 : bond 0.00816 / 0.41 ( 5) link_ALPHA1-3 : angle 2.21664 / 1.37 ( 15) link_ALPHA1-6 : bond 0.00697 / 0.40 ( 5) link_ALPHA1-6 : angle 1.74985 / 1.06 ( 15) link_BETA1-4 : bond 0.00510 / 0.32 ( 13) link_BETA1-4 : angle 1.92185 / 1.27 ( 39) link_NAG-ASN : bond 0.00227 / 0.13 ( 8) link_NAG-ASN : angle 1.86685 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7671 (ptp90) REVERT: A 78 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7105 (mttt) REVERT: A 120 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7314 (mtt-85) REVERT: B 18 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8194 (ttmm) REVERT: B 49 MET cc_start: 0.8119 (mtp) cc_final: 0.7484 (pp-130) REVERT: B 215 LYS cc_start: 0.8821 (tttt) cc_final: 0.8385 (tptp) REVERT: D 40 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8763 (mtt) REVERT: D 224 GLN cc_start: 0.8702 (mm110) cc_final: 0.8435 (mp10) REVERT: D 227 MET cc_start: 0.8625 (ttt) cc_final: 0.8405 (ttt) REVERT: D 286 MET cc_start: 0.8590 (tpt) cc_final: 0.8293 (tpt) REVERT: C 277 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6596 (mt) REVERT: E 215 LYS cc_start: 0.8939 (tttt) cc_final: 0.8675 (tptt) REVERT: E 462 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8662 (tp) REVERT: F 46 GLU cc_start: 0.8718 (tt0) cc_final: 0.8369 (tm-30) REVERT: F 73 ASP cc_start: 0.6306 (t0) cc_final: 0.5949 (t0) REVERT: F 82 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7483 (mp0) outliers start: 17 outliers final: 10 residues processed: 208 average time/residue: 1.4533 time to fit residues: 330.3929 Evaluate side-chains 206 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 156 LYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 0.0030 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 ASN D 265 ASN C 308 ASN F 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.084944 restraints weight = 80197.097| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.33 r_work: 0.2786 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15792 Z= 0.102 Angle : 0.505 6.118 21473 Z= 0.262 Chirality : 0.042 0.231 2475 Planarity : 0.004 0.079 2580 Dihedral : 8.108 85.100 2808 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.87 % Allowed : 13.16 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % 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: 1.33 (0.20), residues: 1791 helix: 1.99 (0.21), residues: 595 sheet: 0.58 (0.24), residues: 465 loop : 0.27 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 85 TYR 0.027 0.001 TYR D 299 PHE 0.015 0.001 PHE A 304 TRP 0.007 0.001 TRP C 70 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (15752) covalent geometry : angle 0.49586 / 0.26 (21368) SS BOND : bond 0.00175 / 0.08 ( 6) SS BOND : angle 0.69032 / 0.41 ( 12) hydrogen bonds : bond 0.03587 / 2.45 ( 753) hydrogen bonds : angle 4.35179 / 3.07 ( 2384) metal coordination : bond 0.01180 / 0.59 ( 3) link_ALPHA1-3 : bond 0.00965 / 0.50 ( 5) link_ALPHA1-3 : angle 1.79146 / 1.07 ( 15) link_ALPHA1-6 : bond 0.00871 / 0.48 ( 5) link_ALPHA1-6 : angle 1.71220 / 1.06 ( 15) link_BETA1-4 : bond 0.00394 / 0.22 ( 13) link_BETA1-4 : angle 1.51224 / 1.00 ( 39) link_NAG-ASN : bond 0.00242 / 0.14 ( 8) link_NAG-ASN : angle 1.36649 / 0.87 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7678 (ptp90) REVERT: A 78 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7110 (mttt) REVERT: A 120 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7188 (mtt-85) REVERT: A 170 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: B 18 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8193 (ttmm) REVERT: B 49 MET cc_start: 0.8081 (mtp) cc_final: 0.7617 (pp-130) REVERT: B 215 LYS cc_start: 0.8788 (tttt) cc_final: 0.8361 (tptp) REVERT: D 40 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8647 (mtt) REVERT: D 224 GLN cc_start: 0.8635 (mm110) cc_final: 0.8391 (mp10) REVERT: D 227 MET cc_start: 0.8561 (ttt) cc_final: 0.8360 (ttt) REVERT: D 286 MET cc_start: 0.8475 (tpt) cc_final: 0.8205 (tpt) REVERT: C 24 ASP cc_start: 0.7808 (m-30) cc_final: 0.7443 (p0) REVERT: C 277 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6564 (mt) REVERT: E 215 LYS cc_start: 0.8885 (tttt) cc_final: 0.8622 (tptt) REVERT: E 462 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8629 (tp) REVERT: F 46 GLU cc_start: 0.8695 (tt0) cc_final: 0.8343 (tm-30) REVERT: F 73 ASP cc_start: 0.6304 (t0) cc_final: 0.6013 (t0) REVERT: F 82 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7499 (mp0) outliers start: 13 outliers final: 4 residues processed: 215 average time/residue: 1.4156 time to fit residues: 332.5015 Evaluate side-chains 204 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 113 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 ASN D 265 ASN F 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.084269 restraints weight = 89530.636| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.55 r_work: 0.2776 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15792 Z= 0.108 Angle : 0.502 6.135 21473 Z= 0.260 Chirality : 0.041 0.233 2475 Planarity : 0.004 0.079 2580 Dihedral : 7.507 84.289 2808 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.81 % Allowed : 13.28 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.29 % 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: 1.43 (0.20), residues: 1791 helix: 2.10 (0.21), residues: 595 sheet: 0.63 (0.24), residues: 466 loop : 0.31 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 85 TYR 0.026 0.001 TYR D 299 PHE 0.015 0.001 PHE A 304 TRP 0.007 0.001 TRP C 70 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (15752) covalent geometry : angle 0.49102 / 0.26 (21368) SS BOND : bond 0.00252 / 0.12 ( 6) SS BOND : angle 0.83380 / 0.49 ( 12) hydrogen bonds : bond 0.03482 / 2.39 ( 753) hydrogen bonds : angle 4.28732 / 3.03 ( 2384) metal coordination : bond 0.00522 / 0.21 ( 3) link_ALPHA1-3 : bond 0.00889 / 0.47 ( 5) link_ALPHA1-3 : angle 1.84027 / 1.09 ( 15) link_ALPHA1-6 : bond 0.00800 / 0.45 ( 5) link_ALPHA1-6 : angle 1.98987 / 1.15 ( 15) link_BETA1-4 : bond 0.00402 / 0.23 ( 13) link_BETA1-4 : angle 1.53029 / 1.03 ( 39) link_NAG-ASN : bond 0.00226 / 0.12 ( 8) link_NAG-ASN : angle 1.36933 / 0.88 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11178.49 seconds wall clock time: 189 minutes 22.20 seconds (11362.20 seconds total)