Starting phenix.real_space_refine on Tue Aug 26 04:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v89_43031/08_2025/8v89_43031_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v89_43031/08_2025/8v89_43031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v89_43031/08_2025/8v89_43031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v89_43031/08_2025/8v89_43031.map" model { file = "/net/cci-nas-00/data/ceres_data/8v89_43031/08_2025/8v89_43031_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v89_43031/08_2025/8v89_43031_trim.cif" } resolution = 2.53 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= 0.000 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 S 115 5.16 5 C 11030 2.51 5 N 2615 2.21 5 O 3105 1.98 5 H 15855 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32725 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "B" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "C" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "D" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "E" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 9.05, per 1000 atoms: 0.28 Number of scatterers: 32725 At special positions: 0 Unit cell: (98.175, 99, 164.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 5 15.00 O 3105 8.00 N 2615 7.00 C 11030 6.00 H 15855 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 67 " " NAG B 602 " - " ASN B 67 " " NAG C 602 " - " ASN C 67 " " NAG D 602 " - " ASN D 67 " " NAG E 602 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 238.4 nanoseconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 45.2% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.595A pdb=" N LYS A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.859A pdb=" N LEU A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.589A pdb=" N SER A 235 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 236' Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 409 through 467 removed outlier: 4.078A pdb=" N ALA A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.596A pdb=" N LYS B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.859A pdb=" N LEU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.588A pdb=" N SER B 235 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 236 " --> pdb=" O ALA B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 236' Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 409 through 467 removed outlier: 4.077A pdb=" N ALA B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.596A pdb=" N LYS C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.859A pdb=" N LEU C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.589A pdb=" N SER C 235 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 236 " --> pdb=" O ALA C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 236' Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 409 through 467 removed outlier: 4.077A pdb=" N ALA C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.596A pdb=" N LYS D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.860A pdb=" N LEU D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.588A pdb=" N SER D 235 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 232 through 236' Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 409 through 467 removed outlier: 4.077A pdb=" N ALA D 467 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 12 removed outlier: 3.595A pdb=" N LYS E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.859A pdb=" N LEU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 232 through 236 removed outlier: 3.588A pdb=" N SER E 235 " --> pdb=" O PRO E 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY E 236 " --> pdb=" O ALA E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 232 through 236' Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.619A pdb=" N LEU E 254 " --> pdb=" O THR E 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 409 through 467 removed outlier: 4.078A pdb=" N ALA E 467 " --> pdb=" O ILE E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.164A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.164A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.165A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 6.928A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 931 hydrogen bonds defined for protein. 2733 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: 7.14 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15820 1.04 - 1.24: 2110 1.24 - 1.44: 5321 1.44 - 1.64: 9709 1.64 - 1.84: 170 Bond restraints: 33130 Sorted by residual: bond pdb=" NZ LYS B 303 " pdb=" HZ3 LYS B 303 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS D 412 " pdb=" HZ2 LYS D 412 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS E 45 " pdb=" HZ3 LYS E 45 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS B 5 " pdb=" HZ3 LYS B 5 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS C 5 " pdb=" HZ1 LYS C 5 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 33125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 49632 1.48 - 2.97: 6630 2.97 - 4.45: 3007 4.45 - 5.94: 231 5.94 - 7.42: 60 Bond angle restraints: 59560 Sorted by residual: angle pdb=" N ASN D 110 " pdb=" CA ASN D 110 " pdb=" CB ASN D 110 " ideal model delta sigma weight residual 110.51 117.28 -6.77 1.61e+00 3.86e-01 1.77e+01 angle pdb=" N ASN A 110 " pdb=" CA ASN A 110 " pdb=" CB ASN A 110 " ideal model delta sigma weight residual 110.51 117.28 -6.77 1.61e+00 3.86e-01 1.77e+01 angle pdb=" N ASN C 110 " pdb=" CA ASN C 110 " pdb=" CB ASN C 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 angle pdb=" N ASN B 110 " pdb=" CA ASN B 110 " pdb=" CB ASN B 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 angle pdb=" N ASN E 110 " pdb=" CA ASN E 110 " pdb=" CB ASN E 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 ... (remaining 59555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 15705 25.04 - 50.08: 635 50.08 - 75.13: 150 75.13 - 100.17: 35 100.17 - 125.21: 15 Dihedral angle restraints: 16540 sinusoidal: 9345 harmonic: 7195 Sorted by residual: dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual 180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 16537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2529 0.101 - 0.203: 156 0.203 - 0.304: 5 0.304 - 0.405: 0 0.405 - 0.506: 5 Chirality restraints: 2695 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.51e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.42e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.40e+01 ... (remaining 2692 not shown) Planarity restraints: 4700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.316 2.00e-02 2.50e+03 2.73e-01 9.32e+02 pdb=" C7 NAG L 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.475 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.315 2.00e-02 2.50e+03 2.73e-01 9.32e+02 pdb=" C7 NAG F 2 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.315 2.00e-02 2.50e+03 2.73e-01 9.31e+02 pdb=" C7 NAG H 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.202 2.00e-02 2.50e+03 ... (remaining 4697 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1842 2.20 - 2.80: 65388 2.80 - 3.40: 91293 3.40 - 4.00: 125052 4.00 - 4.60: 187670 Nonbonded interactions: 471245 Sorted by model distance: nonbonded pdb=" OD2 ASP D 81 " pdb=" HD1 HIS D 104 " model vdw 1.604 2.450 nonbonded pdb=" OD2 ASP A 81 " pdb=" HD1 HIS A 104 " model vdw 1.604 2.450 nonbonded pdb=" OD2 ASP E 81 " pdb=" HD1 HIS E 104 " model vdw 1.604 2.450 nonbonded pdb=" OD2 ASP C 81 " pdb=" HD1 HIS C 104 " model vdw 1.604 2.450 nonbonded pdb=" OD2 ASP B 81 " pdb=" HD1 HIS B 104 " model vdw 1.604 2.450 ... (remaining 471240 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'B' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'D' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'E' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 32.410 Find NCS groups from input model: 0.700 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.008 0.080 17305 Z= 0.376 Angle : 1.003 7.928 23605 Z= 0.537 Chirality : 0.056 0.506 2695 Planarity : 0.014 0.273 2825 Dihedral : 15.417 125.211 7155 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.56 % Allowed : 1.68 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.16), residues: 1960 helix: -1.22 (0.15), residues: 790 sheet: -1.05 (0.21), residues: 440 loop : -0.86 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 206 TYR 0.017 0.004 TYR B 194 PHE 0.020 0.003 PHE E 186 TRP 0.012 0.002 TRP D 437 HIS 0.006 0.002 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00783 (17270) covalent geometry : angle 0.98343 (23510) SS BOND : bond 0.00823 ( 10) SS BOND : angle 2.02258 ( 20) hydrogen bonds : bond 0.16329 ( 826) hydrogen bonds : angle 7.49653 ( 2733) link_BETA1-4 : bond 0.01758 ( 10) link_BETA1-4 : angle 1.66889 ( 30) link_NAG-ASN : bond 0.02648 ( 15) link_NAG-ASN : angle 4.36515 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 377 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8474 (mpt90) REVERT: B 18 GLU cc_start: 0.8062 (tt0) cc_final: 0.7857 (tt0) REVERT: B 274 PHE cc_start: 0.7351 (m-10) cc_final: 0.7067 (m-10) REVERT: C 249 LEU cc_start: 0.8504 (tp) cc_final: 0.8242 (tm) REVERT: D 160 GLN cc_start: 0.8259 (mt0) cc_final: 0.8046 (mt0) REVERT: D 186 PHE cc_start: 0.7588 (m-80) cc_final: 0.7340 (m-80) REVERT: D 238 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8739 (mtpp) REVERT: E 92 TYR cc_start: 0.8519 (m-10) cc_final: 0.8282 (m-10) REVERT: E 455 PHE cc_start: 0.7557 (t80) cc_final: 0.7146 (t80) outliers start: 10 outliers final: 1 residues processed: 387 average time/residue: 0.8836 time to fit residues: 390.5623 Evaluate side-chains 336 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain D residue 238 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 47 GLN B 160 GLN B 293 GLN C 47 GLN C 293 GLN D 26 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.155063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.136360 restraints weight = 62161.407| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.37 r_work: 0.3268 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17305 Z= 0.152 Angle : 0.655 5.807 23605 Z= 0.339 Chirality : 0.042 0.153 2695 Planarity : 0.005 0.057 2825 Dihedral : 12.319 120.442 3387 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.79 % Allowed : 8.04 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.17), residues: 1960 helix: 0.94 (0.17), residues: 810 sheet: -0.53 (0.21), residues: 445 loop : -0.37 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 446 TYR 0.012 0.002 TYR C 150 PHE 0.022 0.002 PHE A 99 TRP 0.007 0.001 TRP D 173 HIS 0.002 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00322 (17270) covalent geometry : angle 0.63930 (23510) SS BOND : bond 0.00725 ( 10) SS BOND : angle 1.32061 ( 20) hydrogen bonds : bond 0.05348 ( 826) hydrogen bonds : angle 5.47830 ( 2733) link_BETA1-4 : bond 0.00160 ( 10) link_BETA1-4 : angle 1.79005 ( 30) link_NAG-ASN : bond 0.00670 ( 15) link_NAG-ASN : angle 2.95092 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 360 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8550 (mpt90) REVERT: A 216 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 216 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7662 (mp) REVERT: B 294 TYR cc_start: 0.8784 (m-80) cc_final: 0.8494 (m-80) REVERT: B 298 ASP cc_start: 0.8174 (t0) cc_final: 0.7907 (t0) REVERT: B 450 MET cc_start: 0.6995 (mmm) cc_final: 0.6742 (mmm) REVERT: C 18 GLU cc_start: 0.8252 (tt0) cc_final: 0.7917 (tt0) REVERT: C 75 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8226 (mtpm) REVERT: C 294 TYR cc_start: 0.8735 (m-80) cc_final: 0.8519 (m-80) REVERT: C 472 GLU cc_start: 0.7545 (tt0) cc_final: 0.7219 (tt0) REVERT: D 216 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7684 (mp) REVERT: D 446 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7884 (tpp80) REVERT: E 212 LEU cc_start: 0.8191 (mt) cc_final: 0.7857 (mm) REVERT: E 216 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7554 (mp) REVERT: E 455 PHE cc_start: 0.7828 (t80) cc_final: 0.7434 (t80) outliers start: 32 outliers final: 11 residues processed: 377 average time/residue: 0.8132 time to fit residues: 354.4623 Evaluate side-chains 355 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 339 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 11 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 156 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 160 GLN D 47 GLN E 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.151406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.132212 restraints weight = 62312.321| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.45 r_work: 0.3222 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17305 Z= 0.212 Angle : 0.688 12.435 23605 Z= 0.350 Chirality : 0.042 0.149 2695 Planarity : 0.005 0.053 2825 Dihedral : 11.884 114.383 3383 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.29 % Allowed : 8.77 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.18), residues: 1960 helix: 1.33 (0.17), residues: 845 sheet: -0.53 (0.21), residues: 435 loop : -0.31 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 206 TYR 0.012 0.002 TYR A 31 PHE 0.015 0.002 PHE C 470 TRP 0.008 0.001 TRP E 148 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00463 (17270) covalent geometry : angle 0.66516 (23510) SS BOND : bond 0.00699 ( 10) SS BOND : angle 1.37104 ( 20) hydrogen bonds : bond 0.05232 ( 826) hydrogen bonds : angle 5.31490 ( 2733) link_BETA1-4 : bond 0.00441 ( 10) link_BETA1-4 : angle 1.83736 ( 30) link_NAG-ASN : bond 0.00650 ( 15) link_NAG-ASN : angle 3.74504 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8364 (tt0) cc_final: 0.8162 (tt0) REVERT: A 78 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8527 (mpt90) REVERT: A 216 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7805 (mp) REVERT: B 450 MET cc_start: 0.6988 (mmm) cc_final: 0.6691 (mmm) REVERT: B 472 GLU cc_start: 0.7755 (tt0) cc_final: 0.7436 (tt0) REVERT: C 75 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8259 (mtpm) REVERT: C 294 TYR cc_start: 0.8842 (m-80) cc_final: 0.8625 (m-80) REVERT: C 472 GLU cc_start: 0.7594 (tt0) cc_final: 0.7164 (tt0) REVERT: D 216 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7730 (mp) REVERT: D 446 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7887 (tpp80) REVERT: E 92 TYR cc_start: 0.8582 (m-10) cc_final: 0.8313 (m-10) REVERT: E 212 LEU cc_start: 0.8264 (mt) cc_final: 0.7931 (mm) REVERT: E 216 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7631 (mp) REVERT: E 278 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6461 (mpt) REVERT: E 455 PHE cc_start: 0.7843 (t80) cc_final: 0.7440 (t80) outliers start: 38 outliers final: 14 residues processed: 360 average time/residue: 1.0075 time to fit residues: 415.6625 Evaluate side-chains 349 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 330 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN D 47 GLN E 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.153535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.132428 restraints weight = 62065.803| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.30 r_work: 0.3265 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17305 Z= 0.142 Angle : 0.598 9.987 23605 Z= 0.302 Chirality : 0.040 0.149 2695 Planarity : 0.005 0.053 2825 Dihedral : 10.992 110.045 3383 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.96 % Allowed : 10.11 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.18), residues: 1960 helix: 1.99 (0.17), residues: 815 sheet: -0.23 (0.22), residues: 455 loop : -0.11 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 206 TYR 0.010 0.002 TYR A 419 PHE 0.012 0.001 PHE C 470 TRP 0.006 0.001 TRP C 133 HIS 0.002 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00304 (17270) covalent geometry : angle 0.57418 (23510) SS BOND : bond 0.00691 ( 10) SS BOND : angle 1.27359 ( 20) hydrogen bonds : bond 0.04610 ( 826) hydrogen bonds : angle 5.06531 ( 2733) link_BETA1-4 : bond 0.00156 ( 10) link_BETA1-4 : angle 1.49731 ( 30) link_NAG-ASN : bond 0.00463 ( 15) link_NAG-ASN : angle 3.58418 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 347 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8522 (mpt90) REVERT: A 212 LEU cc_start: 0.8161 (mt) cc_final: 0.7861 (mm) REVERT: A 216 ILE cc_start: 0.8001 (mp) cc_final: 0.7788 (mm) REVERT: A 278 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6847 (mpt) REVERT: B 294 TYR cc_start: 0.8813 (m-80) cc_final: 0.8582 (m-80) REVERT: B 450 MET cc_start: 0.6915 (mmm) cc_final: 0.6607 (mmm) REVERT: B 472 GLU cc_start: 0.7738 (tt0) cc_final: 0.7393 (tt0) REVERT: C 67 ASN cc_start: 0.7384 (t0) cc_final: 0.7177 (m-40) REVERT: C 69 SER cc_start: 0.7659 (p) cc_final: 0.7162 (p) REVERT: C 75 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8258 (mtpm) REVERT: C 472 GLU cc_start: 0.7551 (tt0) cc_final: 0.7246 (tt0) REVERT: D 274 PHE cc_start: 0.7241 (m-10) cc_final: 0.6779 (m-10) REVERT: D 278 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6622 (mpt) REVERT: D 294 TYR cc_start: 0.8803 (m-80) cc_final: 0.8549 (m-80) REVERT: D 446 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7871 (tpp80) REVERT: E 70 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7510 (mt-10) REVERT: E 92 TYR cc_start: 0.8546 (m-10) cc_final: 0.8248 (m-10) REVERT: E 212 LEU cc_start: 0.8193 (mt) cc_final: 0.7857 (mm) REVERT: E 216 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7579 (mm) REVERT: E 278 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6432 (mpt) REVERT: E 455 PHE cc_start: 0.7859 (t80) cc_final: 0.7437 (t80) outliers start: 30 outliers final: 14 residues processed: 365 average time/residue: 1.0564 time to fit residues: 443.2410 Evaluate side-chains 364 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 345 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 47 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.152664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.133505 restraints weight = 65484.446| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.26 r_work: 0.3226 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17305 Z= 0.232 Angle : 0.675 8.997 23605 Z= 0.344 Chirality : 0.042 0.145 2695 Planarity : 0.005 0.062 2825 Dihedral : 10.852 105.869 3383 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.79 % Allowed : 10.56 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.18), residues: 1960 helix: 1.68 (0.17), residues: 845 sheet: -0.25 (0.22), residues: 445 loop : -0.22 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 206 TYR 0.015 0.002 TYR A 31 PHE 0.015 0.002 PHE A 470 TRP 0.006 0.001 TRP C 148 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00516 (17270) covalent geometry : angle 0.64704 (23510) SS BOND : bond 0.00689 ( 10) SS BOND : angle 1.46668 ( 20) hydrogen bonds : bond 0.05128 ( 826) hydrogen bonds : angle 5.18350 ( 2733) link_BETA1-4 : bond 0.00588 ( 10) link_BETA1-4 : angle 2.10991 ( 30) link_NAG-ASN : bond 0.00612 ( 15) link_NAG-ASN : angle 4.05121 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 338 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8598 (mtt90) REVERT: A 278 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7213 (mpt) REVERT: B 212 LEU cc_start: 0.8258 (mt) cc_final: 0.8050 (mm) REVERT: B 294 TYR cc_start: 0.8810 (m-80) cc_final: 0.8561 (m-80) REVERT: B 450 MET cc_start: 0.7013 (mmm) cc_final: 0.6700 (mmm) REVERT: B 472 GLU cc_start: 0.7822 (tt0) cc_final: 0.7481 (tt0) REVERT: C 69 SER cc_start: 0.7706 (p) cc_final: 0.7355 (p) REVERT: C 75 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8297 (mtpm) REVERT: C 128 TYR cc_start: 0.7475 (t80) cc_final: 0.7132 (t80) REVERT: C 265 ASP cc_start: 0.7507 (t0) cc_final: 0.7299 (t0) REVERT: C 472 GLU cc_start: 0.7602 (tt0) cc_final: 0.7215 (tt0) REVERT: D 278 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6730 (mpt) REVERT: D 294 TYR cc_start: 0.8851 (m-80) cc_final: 0.8500 (m-80) REVERT: D 446 ARG cc_start: 0.8172 (tpp80) cc_final: 0.7914 (tpp80) REVERT: E 92 TYR cc_start: 0.8581 (m-10) cc_final: 0.8286 (m-10) REVERT: E 212 LEU cc_start: 0.8281 (mt) cc_final: 0.8013 (mm) REVERT: E 216 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7674 (mp) REVERT: E 278 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6682 (mpt) REVERT: E 294 TYR cc_start: 0.8774 (m-80) cc_final: 0.8565 (m-80) REVERT: E 455 PHE cc_start: 0.7895 (t80) cc_final: 0.7507 (t80) outliers start: 27 outliers final: 16 residues processed: 353 average time/residue: 1.0460 time to fit residues: 425.5958 Evaluate side-chains 352 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 331 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 47 GLN C 47 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.151525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.132383 restraints weight = 60174.501| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.31 r_work: 0.3221 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17305 Z= 0.199 Angle : 0.664 15.113 23605 Z= 0.332 Chirality : 0.041 0.154 2695 Planarity : 0.005 0.067 2825 Dihedral : 10.568 99.004 3383 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.90 % Allowed : 10.34 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.18), residues: 1960 helix: 1.98 (0.17), residues: 815 sheet: -0.22 (0.22), residues: 435 loop : -0.28 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 206 TYR 0.012 0.002 TYR D 273 PHE 0.014 0.002 PHE C 470 TRP 0.007 0.001 TRP C 133 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00438 (17270) covalent geometry : angle 0.61824 (23510) SS BOND : bond 0.00693 ( 10) SS BOND : angle 1.40473 ( 20) hydrogen bonds : bond 0.04907 ( 826) hydrogen bonds : angle 5.07493 ( 2733) link_BETA1-4 : bond 0.00374 ( 10) link_BETA1-4 : angle 1.89322 ( 30) link_NAG-ASN : bond 0.00587 ( 15) link_NAG-ASN : angle 5.32490 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 341 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8610 (mtt90) REVERT: A 278 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7149 (mpt) REVERT: B 212 LEU cc_start: 0.8233 (mt) cc_final: 0.8011 (mm) REVERT: B 278 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6734 (mpt) REVERT: B 294 TYR cc_start: 0.8822 (m-80) cc_final: 0.8554 (m-80) REVERT: B 450 MET cc_start: 0.6981 (mmm) cc_final: 0.6635 (mmm) REVERT: B 472 GLU cc_start: 0.7787 (tt0) cc_final: 0.7417 (tt0) REVERT: C 67 ASN cc_start: 0.7535 (t0) cc_final: 0.7267 (m-40) REVERT: C 69 SER cc_start: 0.7674 (p) cc_final: 0.7466 (m) REVERT: C 75 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8266 (mtpm) REVERT: C 128 TYR cc_start: 0.7420 (t80) cc_final: 0.7058 (t80) REVERT: C 186 PHE cc_start: 0.7535 (m-80) cc_final: 0.7335 (m-80) REVERT: C 212 LEU cc_start: 0.8331 (mt) cc_final: 0.8072 (mm) REVERT: C 265 ASP cc_start: 0.7488 (t0) cc_final: 0.7242 (t0) REVERT: C 294 TYR cc_start: 0.8888 (m-80) cc_final: 0.8634 (m-80) REVERT: C 472 GLU cc_start: 0.7627 (tt0) cc_final: 0.7249 (tt0) REVERT: D 238 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8307 (mttp) REVERT: D 294 TYR cc_start: 0.8856 (m-80) cc_final: 0.8541 (m-80) REVERT: D 446 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7906 (tpp80) REVERT: E 92 TYR cc_start: 0.8578 (m-10) cc_final: 0.8280 (m-10) REVERT: E 212 LEU cc_start: 0.8284 (mt) cc_final: 0.8019 (mm) REVERT: E 216 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7673 (mp) REVERT: E 278 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6629 (mpt) REVERT: E 455 PHE cc_start: 0.7857 (t80) cc_final: 0.7455 (t80) outliers start: 29 outliers final: 16 residues processed: 353 average time/residue: 1.0674 time to fit residues: 433.6317 Evaluate side-chains 356 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 334 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 26 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.150986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.131801 restraints weight = 61830.404| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.36 r_work: 0.3222 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17305 Z= 0.201 Angle : 0.662 16.155 23605 Z= 0.332 Chirality : 0.041 0.161 2695 Planarity : 0.005 0.070 2825 Dihedral : 10.412 89.105 3383 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.18 % Allowed : 10.39 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 1960 helix: 1.98 (0.17), residues: 815 sheet: -0.18 (0.23), residues: 435 loop : -0.28 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 206 TYR 0.013 0.002 TYR A 31 PHE 0.015 0.002 PHE E 470 TRP 0.007 0.001 TRP C 133 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00442 (17270) covalent geometry : angle 0.61681 (23510) SS BOND : bond 0.00693 ( 10) SS BOND : angle 1.42250 ( 20) hydrogen bonds : bond 0.04882 ( 826) hydrogen bonds : angle 5.05433 ( 2733) link_BETA1-4 : bond 0.00426 ( 10) link_BETA1-4 : angle 2.05287 ( 30) link_NAG-ASN : bond 0.00575 ( 15) link_NAG-ASN : angle 5.20668 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 341 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8617 (mtt90) REVERT: A 278 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7241 (mtm) REVERT: B 212 LEU cc_start: 0.8265 (mt) cc_final: 0.8030 (mm) REVERT: B 294 TYR cc_start: 0.8831 (m-80) cc_final: 0.8575 (m-80) REVERT: B 450 MET cc_start: 0.6972 (mmm) cc_final: 0.6625 (mmm) REVERT: B 472 GLU cc_start: 0.7768 (tt0) cc_final: 0.7396 (tt0) REVERT: C 67 ASN cc_start: 0.7569 (t0) cc_final: 0.7252 (m-40) REVERT: C 69 SER cc_start: 0.7647 (p) cc_final: 0.7105 (p) REVERT: C 128 TYR cc_start: 0.7428 (t80) cc_final: 0.7114 (t80) REVERT: C 212 LEU cc_start: 0.8321 (mt) cc_final: 0.8072 (mm) REVERT: C 294 TYR cc_start: 0.8880 (m-80) cc_final: 0.8616 (m-80) REVERT: C 455 PHE cc_start: 0.7883 (t80) cc_final: 0.7624 (t80) REVERT: C 472 GLU cc_start: 0.7624 (tt0) cc_final: 0.7217 (tt0) REVERT: D 67 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.7016 (m-40) REVERT: D 97 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: D 294 TYR cc_start: 0.8867 (m-80) cc_final: 0.8537 (m-80) REVERT: D 446 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7887 (tpp80) REVERT: E 92 TYR cc_start: 0.8577 (m-10) cc_final: 0.8283 (m-10) REVERT: E 181 LYS cc_start: 0.8169 (tttt) cc_final: 0.7915 (tmtt) REVERT: E 212 LEU cc_start: 0.8284 (mt) cc_final: 0.8027 (mm) REVERT: E 254 LEU cc_start: 0.7629 (mt) cc_final: 0.7404 (mt) REVERT: E 278 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6618 (mpt) REVERT: E 455 PHE cc_start: 0.7851 (t80) cc_final: 0.7432 (t80) outliers start: 34 outliers final: 18 residues processed: 356 average time/residue: 0.9373 time to fit residues: 383.9855 Evaluate side-chains 368 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 345 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 99 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 427 GLN C 26 GLN C 47 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.152079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.130612 restraints weight = 62484.133| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.34 r_work: 0.3248 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17305 Z= 0.173 Angle : 0.629 16.461 23605 Z= 0.316 Chirality : 0.040 0.182 2695 Planarity : 0.005 0.072 2825 Dihedral : 10.150 75.303 3383 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.68 % Allowed : 11.23 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.18), residues: 1960 helix: 2.10 (0.17), residues: 815 sheet: -0.13 (0.23), residues: 435 loop : -0.24 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 206 TYR 0.012 0.002 TYR D 273 PHE 0.014 0.002 PHE E 470 TRP 0.007 0.001 TRP C 133 HIS 0.002 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00378 (17270) covalent geometry : angle 0.58722 (23510) SS BOND : bond 0.00687 ( 10) SS BOND : angle 1.34758 ( 20) hydrogen bonds : bond 0.04668 ( 826) hydrogen bonds : angle 4.95553 ( 2733) link_BETA1-4 : bond 0.00317 ( 10) link_BETA1-4 : angle 1.89762 ( 30) link_NAG-ASN : bond 0.00500 ( 15) link_NAG-ASN : angle 4.91546 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8622 (mtt90) REVERT: A 212 LEU cc_start: 0.8172 (mt) cc_final: 0.7837 (mm) REVERT: A 278 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7254 (mtm) REVERT: A 428 ASP cc_start: 0.8034 (m-30) cc_final: 0.7804 (m-30) REVERT: B 212 LEU cc_start: 0.8196 (mt) cc_final: 0.7970 (mm) REVERT: B 294 TYR cc_start: 0.8837 (m-80) cc_final: 0.8619 (m-80) REVERT: B 450 MET cc_start: 0.6968 (mmm) cc_final: 0.6616 (mmm) REVERT: B 472 GLU cc_start: 0.7765 (tt0) cc_final: 0.7419 (tt0) REVERT: C 69 SER cc_start: 0.7646 (p) cc_final: 0.7445 (p) REVERT: C 128 TYR cc_start: 0.7430 (t80) cc_final: 0.7084 (t80) REVERT: C 212 LEU cc_start: 0.8288 (mt) cc_final: 0.8041 (mm) REVERT: C 294 TYR cc_start: 0.8905 (m-80) cc_final: 0.8620 (m-80) REVERT: C 455 PHE cc_start: 0.7863 (t80) cc_final: 0.7617 (t80) REVERT: C 472 GLU cc_start: 0.7631 (tt0) cc_final: 0.7246 (tt0) REVERT: D 97 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: D 294 TYR cc_start: 0.8846 (m-80) cc_final: 0.8549 (m-80) REVERT: D 446 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7912 (tpp80) REVERT: E 92 TYR cc_start: 0.8572 (m-10) cc_final: 0.8277 (m-10) REVERT: E 212 LEU cc_start: 0.8288 (mt) cc_final: 0.8016 (mm) REVERT: E 254 LEU cc_start: 0.7638 (mt) cc_final: 0.7405 (mt) REVERT: E 455 PHE cc_start: 0.7834 (t80) cc_final: 0.7426 (t80) outliers start: 25 outliers final: 16 residues processed: 361 average time/residue: 0.8476 time to fit residues: 353.9915 Evaluate side-chains 354 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 335 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 146 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 47 GLN D 47 GLN D 158 GLN E 26 GLN E 47 GLN ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.150586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.131381 restraints weight = 58831.639| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.30 r_work: 0.3222 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17305 Z= 0.246 Angle : 0.721 19.736 23605 Z= 0.359 Chirality : 0.043 0.224 2695 Planarity : 0.006 0.075 2825 Dihedral : 10.162 75.298 3383 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.56 % Allowed : 11.51 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.18), residues: 1960 helix: 1.91 (0.17), residues: 795 sheet: -0.10 (0.23), residues: 435 loop : -0.26 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 206 TYR 0.018 0.003 TYR A 31 PHE 0.018 0.002 PHE A 186 TRP 0.008 0.002 TRP D 148 HIS 0.003 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00545 (17270) covalent geometry : angle 0.66629 (23510) SS BOND : bond 0.00682 ( 10) SS BOND : angle 1.52371 ( 20) hydrogen bonds : bond 0.05147 ( 826) hydrogen bonds : angle 5.13678 ( 2733) link_BETA1-4 : bond 0.00555 ( 10) link_BETA1-4 : angle 2.48081 ( 30) link_NAG-ASN : bond 0.00745 ( 15) link_NAG-ASN : angle 5.93879 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 330 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8794 (mpt90) REVERT: B 212 LEU cc_start: 0.8278 (mt) cc_final: 0.8052 (mm) REVERT: B 238 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8697 (mttp) REVERT: B 294 TYR cc_start: 0.8818 (m-80) cc_final: 0.8588 (m-80) REVERT: B 450 MET cc_start: 0.7066 (mmm) cc_final: 0.6720 (mmm) REVERT: B 472 GLU cc_start: 0.7780 (tt0) cc_final: 0.7424 (tt0) REVERT: C 97 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: C 128 TYR cc_start: 0.7486 (t80) cc_final: 0.7182 (t80) REVERT: C 185 ARG cc_start: 0.6791 (tpp80) cc_final: 0.6469 (tpp80) REVERT: C 212 LEU cc_start: 0.8339 (mt) cc_final: 0.8106 (mm) REVERT: C 263 THR cc_start: 0.7885 (t) cc_final: 0.7614 (m) REVERT: C 294 TYR cc_start: 0.8939 (m-80) cc_final: 0.8601 (m-80) REVERT: C 455 PHE cc_start: 0.7860 (t80) cc_final: 0.7642 (t80) REVERT: C 472 GLU cc_start: 0.7673 (tt0) cc_final: 0.7273 (tt0) REVERT: D 294 TYR cc_start: 0.8894 (m-80) cc_final: 0.8515 (m-80) REVERT: D 446 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7925 (tpp80) REVERT: E 92 TYR cc_start: 0.8589 (m-10) cc_final: 0.8273 (m-10) REVERT: E 212 LEU cc_start: 0.8325 (mt) cc_final: 0.8074 (mm) REVERT: E 254 LEU cc_start: 0.7677 (mt) cc_final: 0.7453 (mt) REVERT: E 455 PHE cc_start: 0.7849 (t80) cc_final: 0.7430 (t80) outliers start: 23 outliers final: 15 residues processed: 342 average time/residue: 0.8920 time to fit residues: 352.2627 Evaluate side-chains 344 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 326 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 26 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.154994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.133915 restraints weight = 62377.731| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.35 r_work: 0.3273 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17305 Z= 0.138 Angle : 0.618 19.000 23605 Z= 0.305 Chirality : 0.040 0.190 2695 Planarity : 0.005 0.076 2825 Dihedral : 9.559 75.703 3383 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.23 % Allowed : 12.07 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.19), residues: 1960 helix: 2.21 (0.17), residues: 810 sheet: 0.07 (0.23), residues: 455 loop : -0.12 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 206 TYR 0.008 0.001 TYR A 419 PHE 0.013 0.001 PHE E 470 TRP 0.008 0.001 TRP C 133 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00297 (17270) covalent geometry : angle 0.56663 (23510) SS BOND : bond 0.00691 ( 10) SS BOND : angle 1.28969 ( 20) hydrogen bonds : bond 0.04423 ( 826) hydrogen bonds : angle 4.84283 ( 2733) link_BETA1-4 : bond 0.00115 ( 10) link_BETA1-4 : angle 1.72166 ( 30) link_NAG-ASN : bond 0.00540 ( 15) link_NAG-ASN : angle 5.44760 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 329 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8772 (mpt90) REVERT: A 428 ASP cc_start: 0.8024 (m-30) cc_final: 0.7786 (m-30) REVERT: B 212 LEU cc_start: 0.8191 (mt) cc_final: 0.7959 (mm) REVERT: B 278 MET cc_start: 0.7272 (mmt) cc_final: 0.7055 (mtm) REVERT: B 294 TYR cc_start: 0.8828 (m-80) cc_final: 0.8609 (m-80) REVERT: B 450 MET cc_start: 0.6947 (mmm) cc_final: 0.6597 (mmm) REVERT: B 472 GLU cc_start: 0.7715 (tt0) cc_final: 0.7420 (tt0) REVERT: C 128 TYR cc_start: 0.7473 (t80) cc_final: 0.7151 (t80) REVERT: C 212 LEU cc_start: 0.8252 (mt) cc_final: 0.8015 (mm) REVERT: C 455 PHE cc_start: 0.7830 (t80) cc_final: 0.7627 (t80) REVERT: C 472 GLU cc_start: 0.7613 (tt0) cc_final: 0.7291 (tt0) REVERT: D 294 TYR cc_start: 0.8862 (m-80) cc_final: 0.8572 (m-80) REVERT: D 446 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7907 (tpp80) REVERT: E 44 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.5685 (mm-30) REVERT: E 92 TYR cc_start: 0.8547 (m-10) cc_final: 0.8325 (m-10) REVERT: E 181 LYS cc_start: 0.8148 (tttt) cc_final: 0.7879 (tmtt) REVERT: E 212 LEU cc_start: 0.8202 (mt) cc_final: 0.7942 (mm) REVERT: E 216 ILE cc_start: 0.7830 (mp) cc_final: 0.7629 (mm) REVERT: E 254 LEU cc_start: 0.7658 (mt) cc_final: 0.7432 (mt) REVERT: E 455 PHE cc_start: 0.7806 (t80) cc_final: 0.7399 (t80) outliers start: 17 outliers final: 12 residues processed: 342 average time/residue: 0.8735 time to fit residues: 345.9791 Evaluate side-chains 343 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 329 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 119 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 139 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN D 47 GLN E 47 GLN E 56 GLN A Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.153905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.132626 restraints weight = 59560.329| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.32 r_work: 0.3258 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17305 Z= 0.134 Angle : 0.596 15.463 23605 Z= 0.297 Chirality : 0.040 0.275 2695 Planarity : 0.005 0.072 2825 Dihedral : 9.307 78.689 3383 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.06 % Allowed : 12.29 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.19), residues: 1960 helix: 2.39 (0.17), residues: 815 sheet: 0.12 (0.23), residues: 450 loop : -0.06 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 206 TYR 0.009 0.001 TYR D 273 PHE 0.013 0.001 PHE C 470 TRP 0.008 0.001 TRP C 133 HIS 0.002 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00290 (17270) covalent geometry : angle 0.55843 (23510) SS BOND : bond 0.00703 ( 10) SS BOND : angle 1.23494 ( 20) hydrogen bonds : bond 0.04290 ( 826) hydrogen bonds : angle 4.74695 ( 2733) link_BETA1-4 : bond 0.00186 ( 10) link_BETA1-4 : angle 1.78786 ( 30) link_NAG-ASN : bond 0.00673 ( 15) link_NAG-ASN : angle 4.56137 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11507.29 seconds wall clock time: 195 minutes 7.83 seconds (11707.83 seconds total)