Starting phenix.real_space_refine on Sat Jun 28 19:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v89_43031/06_2025/8v89_43031_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v89_43031/06_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_43031/06_2025/8v89_43031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v89_43031/06_2025/8v89_43031.map" model { file = "/net/cci-nas-00/data/ceres_data/8v89_43031/06_2025/8v89_43031_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v89_43031/06_2025/8v89_43031_trim.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 28.43, per 1000 atoms: 0.87 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: 8.86 Conformation dependent library (CDL) restraints added in 4.3 seconds 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: 2.77 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: 13.38 Time building geometry restraints manager: 10.68 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: 0.03 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: 2.720 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: 0.550 Extract box with map and model: 1.230 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 85.090 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP D 437 HIS 0.006 0.002 HIS B 296 PHE 0.020 0.003 PHE E 186 TYR 0.017 0.004 TYR B 194 ARG 0.009 0.001 ARG C 206 Details of bonding type rmsd link_NAG-ASN : bond 0.02648 ( 15) link_NAG-ASN : angle 4.36515 ( 45) link_BETA1-4 : bond 0.01758 ( 10) link_BETA1-4 : angle 1.66889 ( 30) hydrogen bonds : bond 0.16329 ( 826) hydrogen bonds : angle 7.49653 ( 2733) SS BOND : bond 0.00823 ( 10) SS BOND : angle 2.02258 ( 20) covalent geometry : bond 0.00783 (17270) covalent geometry : angle 0.98343 (23510) *********************** 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 : 2.506 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: 2.0969 time to fit residues: 928.7570 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 : 2.341 ------------------------------------------------------------------------------- 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 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.155050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.136654 restraints weight = 57471.913| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.20 r_work: 0.3303 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17305 Z= 0.155 Angle : 0.657 5.688 23605 Z= 0.339 Chirality : 0.043 0.158 2695 Planarity : 0.005 0.060 2825 Dihedral : 12.242 120.191 3387 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.84 % Allowed : 7.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 1960 helix: 0.97 (0.17), residues: 810 sheet: -0.53 (0.21), residues: 445 loop : -0.35 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 173 HIS 0.002 0.001 HIS E 104 PHE 0.021 0.002 PHE A 99 TYR 0.012 0.002 TYR C 150 ARG 0.008 0.001 ARG E 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 15) link_NAG-ASN : angle 2.92106 ( 45) link_BETA1-4 : bond 0.00357 ( 10) link_BETA1-4 : angle 1.93343 ( 30) hydrogen bonds : bond 0.05231 ( 826) hydrogen bonds : angle 5.42813 ( 2733) SS BOND : bond 0.00722 ( 10) SS BOND : angle 1.30023 ( 20) covalent geometry : bond 0.00329 (17270) covalent geometry : angle 0.64051 (23510) *********************** 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 393 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 360 time to evaluate : 2.334 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: 0.8553 (mpt90) REVERT: A 216 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7646 (mp) REVERT: B 216 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7580 (mp) REVERT: B 294 TYR cc_start: 0.8768 (m-80) cc_final: 0.8521 (m-80) REVERT: B 298 ASP cc_start: 0.8153 (t0) cc_final: 0.7884 (t0) REVERT: B 450 MET cc_start: 0.6933 (mmm) cc_final: 0.6657 (mmm) REVERT: C 18 GLU cc_start: 0.8228 (tt0) cc_final: 0.7882 (tt0) REVERT: C 294 TYR cc_start: 0.8718 (m-80) cc_final: 0.8508 (m-80) REVERT: C 472 GLU cc_start: 0.7537 (tt0) cc_final: 0.7223 (tt0) REVERT: D 216 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7653 (mp) REVERT: D 446 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7875 (tpp80) REVERT: E 212 LEU cc_start: 0.8158 (mt) cc_final: 0.7833 (mm) REVERT: E 216 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7512 (mp) REVERT: E 455 PHE cc_start: 0.7814 (t80) cc_final: 0.7425 (t80) outliers start: 33 outliers final: 11 residues processed: 379 average time/residue: 1.9602 time to fit residues: 857.4190 Evaluate side-chains 358 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 342 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.5980 chunk 159 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 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 = 0.3590 r_free = 0.3590 target = 0.153443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.134001 restraints weight = 65396.525| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.37 r_work: 0.3251 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17305 Z= 0.184 Angle : 0.660 11.248 23605 Z= 0.335 Chirality : 0.041 0.191 2695 Planarity : 0.005 0.055 2825 Dihedral : 11.820 113.797 3383 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.18 % Allowed : 8.88 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 1960 helix: 1.62 (0.17), residues: 815 sheet: -0.43 (0.21), residues: 425 loop : -0.32 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 148 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.002 PHE C 470 TYR 0.012 0.002 TYR A 419 ARG 0.012 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 15) link_NAG-ASN : angle 3.65927 ( 45) link_BETA1-4 : bond 0.00379 ( 10) link_BETA1-4 : angle 1.68881 ( 30) hydrogen bonds : bond 0.05069 ( 826) hydrogen bonds : angle 5.24213 ( 2733) SS BOND : bond 0.00691 ( 10) SS BOND : angle 1.31635 ( 20) covalent geometry : bond 0.00396 (17270) covalent geometry : angle 0.63778 (23510) *********************** 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 377 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 2.345 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 18 GLU cc_start: 0.8358 (tt0) cc_final: 0.8150 (tt0) REVERT: A 78 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8510 (mpt90) REVERT: A 216 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 294 TYR cc_start: 0.8829 (m-80) cc_final: 0.8547 (m-80) REVERT: B 450 MET cc_start: 0.7005 (mmm) cc_final: 0.6712 (mmm) REVERT: B 472 GLU cc_start: 0.7756 (tt0) cc_final: 0.7455 (tt0) REVERT: C 18 GLU cc_start: 0.8289 (tt0) cc_final: 0.7889 (tt0) REVERT: C 43 ASP cc_start: 0.6664 (t70) cc_final: 0.6397 (t0) REVERT: C 472 GLU cc_start: 0.7572 (tt0) cc_final: 0.7232 (tt0) REVERT: D 294 TYR cc_start: 0.8842 (m-80) cc_final: 0.8558 (m-80) REVERT: D 322 MET cc_start: 0.7556 (mtp) cc_final: 0.7339 (mtp) REVERT: D 446 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7913 (tpp80) REVERT: E 92 TYR cc_start: 0.8567 (m-10) cc_final: 0.8316 (m-10) REVERT: E 212 LEU cc_start: 0.8260 (mt) cc_final: 0.7921 (mm) REVERT: E 216 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7613 (mp) REVERT: E 278 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6592 (mpt) REVERT: E 294 TYR cc_start: 0.8746 (m-80) cc_final: 0.8528 (m-80) REVERT: E 455 PHE cc_start: 0.7864 (t80) cc_final: 0.7473 (t80) outliers start: 35 outliers final: 12 residues processed: 361 average time/residue: 1.9573 time to fit residues: 814.1784 Evaluate side-chains 349 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 333 time to evaluate : 2.518 ------------------------------------------------------------------------------- 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 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 290 ILE Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 78 ARG 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 142 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 26 GLN B 160 GLN C 47 GLN D 47 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 = 0.3592 r_free = 0.3592 target = 0.153591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.134767 restraints weight = 59013.701| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.37 r_work: 0.3245 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1827 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= 0.168 Angle : 0.619 9.041 23605 Z= 0.314 Chirality : 0.040 0.148 2695 Planarity : 0.005 0.057 2825 Dihedral : 11.015 106.538 3383 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.01 % Allowed : 9.94 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 1960 helix: 1.96 (0.17), residues: 815 sheet: -0.24 (0.22), residues: 455 loop : -0.18 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.003 0.001 HIS C 104 PHE 0.013 0.002 PHE C 470 TYR 0.012 0.002 TYR A 419 ARG 0.012 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 15) link_NAG-ASN : angle 4.03322 ( 45) link_BETA1-4 : bond 0.00316 ( 10) link_BETA1-4 : angle 1.66031 ( 30) hydrogen bonds : bond 0.04762 ( 826) hydrogen bonds : angle 5.10851 ( 2733) SS BOND : bond 0.00692 ( 10) SS BOND : angle 1.32474 ( 20) covalent geometry : bond 0.00364 (17270) covalent geometry : angle 0.59084 (23510) *********************** 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 371 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 340 time to evaluate : 2.384 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: 0.8894 (OUTLIER) cc_final: 0.8539 (mpt90) REVERT: A 212 LEU cc_start: 0.8211 (mt) cc_final: 0.7907 (mm) REVERT: A 278 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6876 (mpt) REVERT: B 212 LEU cc_start: 0.8195 (mt) cc_final: 0.7955 (mm) REVERT: B 278 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6775 (mpt) REVERT: B 294 TYR cc_start: 0.8825 (m-80) cc_final: 0.8605 (m-80) REVERT: B 450 MET cc_start: 0.6873 (mmm) cc_final: 0.6553 (mmm) REVERT: B 472 GLU cc_start: 0.7704 (tt0) cc_final: 0.7391 (tt0) REVERT: C 43 ASP cc_start: 0.6775 (t70) cc_final: 0.6507 (t0) REVERT: C 67 ASN cc_start: 0.7422 (t0) cc_final: 0.7195 (m-40) REVERT: C 69 SER cc_start: 0.7662 (p) cc_final: 0.7163 (p) REVERT: C 472 GLU cc_start: 0.7580 (tt0) cc_final: 0.7259 (tt0) REVERT: D 274 PHE cc_start: 0.7241 (m-10) cc_final: 0.6721 (m-10) REVERT: D 278 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6675 (mpt) REVERT: D 294 TYR cc_start: 0.8829 (m-80) cc_final: 0.8560 (m-80) REVERT: D 446 ARG cc_start: 0.8120 (tpp80) cc_final: 0.7865 (tpp80) REVERT: E 92 TYR cc_start: 0.8566 (m-10) cc_final: 0.8295 (m-10) REVERT: E 212 LEU cc_start: 0.8227 (mt) cc_final: 0.7912 (mm) REVERT: E 216 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7582 (mm) REVERT: E 278 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6419 (mpt) REVERT: E 455 PHE cc_start: 0.7845 (t80) cc_final: 0.7426 (t80) outliers start: 31 outliers final: 15 residues processed: 358 average time/residue: 1.9419 time to fit residues: 802.4144 Evaluate side-chains 353 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 332 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 B residue 278 MET 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 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 78 ARG 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 172 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 160 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 = 0.3615 r_free = 0.3615 target = 0.155663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.136799 restraints weight = 58828.647| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.43 r_work: 0.3277 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- 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 = 0.41 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: 0.8182 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17305 Z= 0.131 Angle : 0.579 12.443 23605 Z= 0.291 Chirality : 0.040 0.247 2695 Planarity : 0.005 0.070 2825 Dihedral : 10.356 98.454 3383 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.79 % Allowed : 10.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1960 helix: 2.26 (0.17), residues: 820 sheet: -0.16 (0.22), residues: 450 loop : -0.05 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 133 HIS 0.002 0.001 HIS C 104 PHE 0.012 0.001 PHE C 470 TYR 0.009 0.001 TYR A 419 ARG 0.012 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00837 ( 15) link_NAG-ASN : angle 4.33585 ( 45) link_BETA1-4 : bond 0.00118 ( 10) link_BETA1-4 : angle 1.49176 ( 30) hydrogen bonds : bond 0.04399 ( 826) hydrogen bonds : angle 4.91130 ( 2733) SS BOND : bond 0.00691 ( 10) SS BOND : angle 1.26508 ( 20) covalent geometry : bond 0.00282 (17270) covalent geometry : angle 0.54491 (23510) *********************** 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 368 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 341 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8605 (mpt90) REVERT: A 212 LEU cc_start: 0.8193 (mt) cc_final: 0.7892 (mm) REVERT: A 278 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6936 (mpt) REVERT: A 436 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7099 (mm-30) REVERT: B 44 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6124 (tm-30) REVERT: B 212 LEU cc_start: 0.8122 (mt) cc_final: 0.7892 (mm) REVERT: B 450 MET cc_start: 0.6923 (mmm) cc_final: 0.6601 (mmm) REVERT: B 472 GLU cc_start: 0.7722 (tt0) cc_final: 0.7418 (tt0) REVERT: C 43 ASP cc_start: 0.6598 (t70) cc_final: 0.6350 (t0) REVERT: C 47 GLN cc_start: 0.7357 (mm-40) cc_final: 0.7016 (mt0) REVERT: C 69 SER cc_start: 0.7581 (p) cc_final: 0.7261 (p) REVERT: C 455 PHE cc_start: 0.7849 (t80) cc_final: 0.7521 (t80) REVERT: C 472 GLU cc_start: 0.7536 (tt0) cc_final: 0.7301 (tt0) REVERT: D 274 PHE cc_start: 0.7269 (m-10) cc_final: 0.6804 (m-10) REVERT: D 278 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6632 (mpt) REVERT: D 294 TYR cc_start: 0.8798 (m-80) cc_final: 0.8576 (m-80) REVERT: D 446 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7890 (tpp80) REVERT: E 92 TYR cc_start: 0.8545 (m-10) cc_final: 0.8321 (m-10) REVERT: E 212 LEU cc_start: 0.8211 (mt) cc_final: 0.7922 (mm) REVERT: E 278 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6570 (mpt) REVERT: E 455 PHE cc_start: 0.7876 (t80) cc_final: 0.7481 (t80) outliers start: 27 outliers final: 11 residues processed: 356 average time/residue: 2.0697 time to fit residues: 856.4458 Evaluate side-chains 353 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 337 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 44 GLU 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 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 D residue 445 ASP 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 102 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A B 47 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 = 0.3572 r_free = 0.3572 target = 0.151868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.132791 restraints weight = 57498.464| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.37 r_work: 0.3233 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 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 = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17305 Z= 0.209 Angle : 0.658 14.132 23605 Z= 0.330 Chirality : 0.042 0.260 2695 Planarity : 0.005 0.064 2825 Dihedral : 10.341 91.734 3383 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.90 % Allowed : 10.50 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1960 helix: 2.12 (0.17), residues: 815 sheet: -0.20 (0.23), residues: 445 loop : -0.18 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 148 HIS 0.003 0.001 HIS C 104 PHE 0.014 0.002 PHE A 470 TYR 0.013 0.002 TYR A 31 ARG 0.013 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 15) link_NAG-ASN : angle 5.02898 ( 45) link_BETA1-4 : bond 0.00493 ( 10) link_BETA1-4 : angle 2.01542 ( 30) hydrogen bonds : bond 0.04856 ( 826) hydrogen bonds : angle 5.06291 ( 2733) SS BOND : bond 0.00688 ( 10) SS BOND : angle 1.42743 ( 20) covalent geometry : bond 0.00462 (17270) covalent geometry : angle 0.61587 (23510) *********************** 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 368 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 339 time to evaluate : 2.409 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: 0.8978 (OUTLIER) cc_final: 0.8603 (mtt90) REVERT: A 212 LEU cc_start: 0.8172 (mt) cc_final: 0.7915 (mm) REVERT: A 278 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7091 (mpt) REVERT: B 212 LEU cc_start: 0.8232 (mt) cc_final: 0.8000 (mm) REVERT: B 278 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6717 (mpt) REVERT: B 436 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: B 450 MET cc_start: 0.6982 (mmm) cc_final: 0.6636 (mmm) REVERT: B 472 GLU cc_start: 0.7768 (tt0) cc_final: 0.7436 (tt0) REVERT: C 43 ASP cc_start: 0.6795 (t70) cc_final: 0.6514 (t0) REVERT: C 47 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6884 (mt0) REVERT: C 67 ASN cc_start: 0.7515 (t0) cc_final: 0.7254 (m-40) REVERT: C 69 SER cc_start: 0.7639 (p) cc_final: 0.7146 (p) REVERT: C 212 LEU cc_start: 0.8375 (mt) cc_final: 0.8124 (mm) REVERT: C 455 PHE cc_start: 0.7833 (t80) cc_final: 0.7616 (t80) REVERT: C 472 GLU cc_start: 0.7572 (tt0) cc_final: 0.7257 (tt0) REVERT: D 294 TYR cc_start: 0.8834 (m-80) cc_final: 0.8519 (m-80) REVERT: D 446 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7905 (tpp80) REVERT: E 92 TYR cc_start: 0.8585 (m-10) cc_final: 0.8280 (m-10) REVERT: E 181 LYS cc_start: 0.8167 (tttt) cc_final: 0.7931 (tmtt) REVERT: E 212 LEU cc_start: 0.8301 (mt) cc_final: 0.8023 (mm) REVERT: E 278 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6557 (mpt) REVERT: E 455 PHE cc_start: 0.7861 (t80) cc_final: 0.7456 (t80) outliers start: 29 outliers final: 14 residues processed: 350 average time/residue: 2.0629 time to fit residues: 834.3914 Evaluate side-chains 351 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 332 time to evaluate : 2.510 ------------------------------------------------------------------------------- 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 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 B residue 436 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 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 47 GLN B 427 GLN D 26 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 = 0.3593 r_free = 0.3593 target = 0.153774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.135212 restraints weight = 56398.149| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.30 r_work: 0.3290 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17305 Z= 0.130 Angle : 0.600 17.079 23605 Z= 0.295 Chirality : 0.040 0.256 2695 Planarity : 0.004 0.065 2825 Dihedral : 9.973 84.308 3383 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.68 % Allowed : 10.78 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 1960 helix: 2.32 (0.17), residues: 820 sheet: -0.05 (0.23), residues: 450 loop : -0.06 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 133 HIS 0.002 0.001 HIS C 104 PHE 0.011 0.001 PHE E 470 TYR 0.008 0.001 TYR A 419 ARG 0.015 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 15) link_NAG-ASN : angle 5.58927 ( 45) link_BETA1-4 : bond 0.00137 ( 10) link_BETA1-4 : angle 1.54851 ( 30) hydrogen bonds : bond 0.04345 ( 826) hydrogen bonds : angle 4.86079 ( 2733) SS BOND : bond 0.00689 ( 10) SS BOND : angle 1.27759 ( 20) covalent geometry : bond 0.00279 (17270) covalent geometry : angle 0.54467 (23510) *********************** 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 365 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 340 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8582 (mtt90) REVERT: A 212 LEU cc_start: 0.8093 (mt) cc_final: 0.7852 (mm) REVERT: A 278 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7084 (mpt) REVERT: B 75 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8313 (mttm) REVERT: B 97 GLU cc_start: 0.7294 (mp0) cc_final: 0.7027 (tp30) REVERT: B 212 LEU cc_start: 0.8151 (mt) cc_final: 0.7917 (mm) REVERT: B 436 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: B 450 MET cc_start: 0.6921 (mmm) cc_final: 0.6571 (mmm) REVERT: B 472 GLU cc_start: 0.7711 (tt0) cc_final: 0.7407 (tt0) REVERT: C 43 ASP cc_start: 0.6605 (t70) cc_final: 0.6404 (t0) REVERT: C 47 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6868 (mt0) REVERT: C 67 ASN cc_start: 0.7561 (t0) cc_final: 0.7238 (m-40) REVERT: C 69 SER cc_start: 0.7566 (p) cc_final: 0.7079 (p) REVERT: C 212 LEU cc_start: 0.8269 (mt) cc_final: 0.8035 (mm) REVERT: C 472 GLU cc_start: 0.7552 (tt0) cc_final: 0.7327 (tt0) REVERT: D 67 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6879 (m-40) REVERT: D 294 TYR cc_start: 0.8805 (m-80) cc_final: 0.8571 (m-80) REVERT: D 446 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7907 (tpp80) REVERT: E 92 TYR cc_start: 0.8537 (m-10) cc_final: 0.8309 (m-10) REVERT: E 181 LYS cc_start: 0.8149 (tttt) cc_final: 0.7892 (tmtt) REVERT: E 212 LEU cc_start: 0.8203 (mt) cc_final: 0.7939 (mm) REVERT: E 455 PHE cc_start: 0.7837 (t80) cc_final: 0.7438 (t80) outliers start: 25 outliers final: 11 residues processed: 357 average time/residue: 2.1297 time to fit residues: 885.7214 Evaluate side-chains 347 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 332 time to evaluate : 2.306 ------------------------------------------------------------------------------- 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 78 ARG Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 436 GLU 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 270 ILE Chi-restraints excluded: chain D residue 290 ILE 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 180 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN C 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 = 0.3574 r_free = 0.3574 target = 0.152032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.132817 restraints weight = 61588.039| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.37 r_work: 0.3233 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 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 = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17305 Z= 0.189 Angle : 0.646 18.809 23605 Z= 0.322 Chirality : 0.041 0.295 2695 Planarity : 0.005 0.070 2825 Dihedral : 10.128 75.859 3383 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.68 % Allowed : 10.95 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1960 helix: 2.17 (0.17), residues: 820 sheet: -0.15 (0.23), residues: 435 loop : -0.14 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 148 HIS 0.002 0.001 HIS C 104 PHE 0.014 0.002 PHE C 470 TYR 0.013 0.002 TYR A 31 ARG 0.014 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 15) link_NAG-ASN : angle 5.29315 ( 45) link_BETA1-4 : bond 0.00414 ( 10) link_BETA1-4 : angle 2.02373 ( 30) hydrogen bonds : bond 0.04688 ( 826) hydrogen bonds : angle 4.96191 ( 2733) SS BOND : bond 0.00684 ( 10) SS BOND : angle 1.38947 ( 20) covalent geometry : bond 0.00417 (17270) covalent geometry : angle 0.59879 (23510) *********************** 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 367 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 342 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8768 (mpt90) REVERT: A 212 LEU cc_start: 0.8184 (mt) cc_final: 0.7933 (mm) REVERT: A 278 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7155 (mpt) REVERT: B 212 LEU cc_start: 0.8218 (mt) cc_final: 0.7991 (mm) REVERT: B 278 MET cc_start: 0.7311 (mmt) cc_final: 0.7104 (mtm) REVERT: B 450 MET cc_start: 0.6989 (mmm) cc_final: 0.6627 (mmm) REVERT: B 472 GLU cc_start: 0.7749 (tt0) cc_final: 0.7410 (tt0) REVERT: C 43 ASP cc_start: 0.6742 (t70) cc_final: 0.6480 (t0) REVERT: C 47 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6932 (mt0) REVERT: C 128 TYR cc_start: 0.7456 (t80) cc_final: 0.7180 (t80) REVERT: C 212 LEU cc_start: 0.8311 (mt) cc_final: 0.8090 (mm) REVERT: C 265 ASP cc_start: 0.7520 (t0) cc_final: 0.7311 (t0) REVERT: C 472 GLU cc_start: 0.7561 (tt0) cc_final: 0.7256 (tt0) REVERT: D 97 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: D 294 TYR cc_start: 0.8835 (m-80) cc_final: 0.8553 (m-80) REVERT: D 446 ARG cc_start: 0.8145 (tpp80) cc_final: 0.7898 (tpp80) REVERT: E 92 TYR cc_start: 0.8574 (m-10) cc_final: 0.8342 (m-10) REVERT: E 181 LYS cc_start: 0.8173 (tttt) cc_final: 0.7904 (tmtt) REVERT: E 212 LEU cc_start: 0.8276 (mt) cc_final: 0.8018 (mm) REVERT: E 455 PHE cc_start: 0.7741 (t80) cc_final: 0.7359 (t80) outliers start: 25 outliers final: 15 residues processed: 354 average time/residue: 2.0861 time to fit residues: 851.8327 Evaluate side-chains 351 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 333 time to evaluate : 3.039 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain E residue 431 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 47 GLN E 26 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 = 0.3582 r_free = 0.3582 target = 0.152791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.131569 restraints weight = 60206.302| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.31 r_work: 0.3245 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2256 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= 0.172 Angle : 0.638 19.032 23605 Z= 0.316 Chirality : 0.041 0.275 2695 Planarity : 0.005 0.071 2825 Dihedral : 9.899 70.100 3383 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.28 % Allowed : 11.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1960 helix: 2.26 (0.17), residues: 810 sheet: -0.15 (0.23), residues: 435 loop : -0.20 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 133 HIS 0.003 0.001 HIS C 104 PHE 0.013 0.002 PHE A 470 TYR 0.011 0.002 TYR A 31 ARG 0.015 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 15) link_NAG-ASN : angle 5.77378 ( 45) link_BETA1-4 : bond 0.00304 ( 10) link_BETA1-4 : angle 1.86613 ( 30) hydrogen bonds : bond 0.04602 ( 826) hydrogen bonds : angle 4.93412 ( 2733) SS BOND : bond 0.00686 ( 10) SS BOND : angle 1.35622 ( 20) covalent geometry : bond 0.00376 (17270) covalent geometry : angle 0.58228 (23510) *********************** 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 351 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 333 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8614 (mtt90) REVERT: A 212 LEU cc_start: 0.8147 (mt) cc_final: 0.7900 (mm) REVERT: A 278 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7185 (mtm) REVERT: A 436 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 44 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5834 (mm-30) REVERT: B 97 GLU cc_start: 0.7393 (mp0) cc_final: 0.7142 (tp30) REVERT: B 212 LEU cc_start: 0.8174 (mt) cc_final: 0.7948 (mm) REVERT: B 450 MET cc_start: 0.6920 (mmm) cc_final: 0.6550 (mmm) REVERT: B 472 GLU cc_start: 0.7724 (tt0) cc_final: 0.7378 (tt0) REVERT: C 43 ASP cc_start: 0.6698 (t70) cc_final: 0.6440 (t0) REVERT: C 47 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6903 (mt0) REVERT: C 128 TYR cc_start: 0.7457 (t80) cc_final: 0.7180 (t80) REVERT: C 212 LEU cc_start: 0.8305 (mt) cc_final: 0.8087 (mm) REVERT: C 472 GLU cc_start: 0.7560 (tt0) cc_final: 0.7272 (tt0) REVERT: D 97 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: D 294 TYR cc_start: 0.8835 (m-80) cc_final: 0.8545 (m-80) REVERT: D 429 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7250 (mt-10) REVERT: D 446 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7886 (tpp80) REVERT: E 92 TYR cc_start: 0.8578 (m-10) cc_final: 0.8354 (m-10) REVERT: E 181 LYS cc_start: 0.8149 (tttt) cc_final: 0.7871 (tmtt) REVERT: E 212 LEU cc_start: 0.8262 (mt) cc_final: 0.8003 (mm) REVERT: E 455 PHE cc_start: 0.7718 (t80) cc_final: 0.7326 (t80) outliers start: 18 outliers final: 14 residues processed: 345 average time/residue: 2.2109 time to fit residues: 882.9681 Evaluate side-chains 346 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 328 time to evaluate : 2.774 ------------------------------------------------------------------------------- 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 44 GLU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 77 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.155019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.133691 restraints weight = 61275.290| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.34 r_work: 0.3272 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2355 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= 0.126 Angle : 0.574 15.423 23605 Z= 0.286 Chirality : 0.039 0.244 2695 Planarity : 0.005 0.072 2825 Dihedral : 9.347 71.941 3383 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.28 % Allowed : 11.73 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 1960 helix: 2.22 (0.17), residues: 845 sheet: 0.03 (0.23), residues: 450 loop : 0.02 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.001 0.000 HIS B 62 PHE 0.011 0.001 PHE C 470 TYR 0.008 0.001 TYR D 419 ARG 0.015 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 15) link_NAG-ASN : angle 4.82528 ( 45) link_BETA1-4 : bond 0.00113 ( 10) link_BETA1-4 : angle 1.58455 ( 30) hydrogen bonds : bond 0.04173 ( 826) hydrogen bonds : angle 4.72972 ( 2733) SS BOND : bond 0.00686 ( 10) SS BOND : angle 1.24779 ( 20) covalent geometry : bond 0.00275 (17270) covalent geometry : angle 0.53029 (23510) ********************** 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 352 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 334 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8601 (mtt90) REVERT: A 212 LEU cc_start: 0.8145 (mt) cc_final: 0.7864 (mm) REVERT: A 278 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7144 (mtm) REVERT: B 97 GLU cc_start: 0.7369 (mp0) cc_final: 0.7122 (tp30) REVERT: B 212 LEU cc_start: 0.8120 (mt) cc_final: 0.7893 (mm) REVERT: B 450 MET cc_start: 0.6862 (mmm) cc_final: 0.6533 (mmm) REVERT: B 472 GLU cc_start: 0.7658 (tt0) cc_final: 0.7379 (tt0) REVERT: C 43 ASP cc_start: 0.6524 (t70) cc_final: 0.6300 (t0) REVERT: C 47 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6866 (mt0) REVERT: C 128 TYR cc_start: 0.7433 (t80) cc_final: 0.7155 (t80) REVERT: C 212 LEU cc_start: 0.8266 (mt) cc_final: 0.8036 (mm) REVERT: C 322 MET cc_start: 0.7475 (mtp) cc_final: 0.7168 (mtm) REVERT: C 472 GLU cc_start: 0.7424 (tt0) cc_final: 0.7213 (tt0) REVERT: D 294 TYR cc_start: 0.8814 (m-80) cc_final: 0.8543 (m-80) REVERT: D 429 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7243 (mt-10) REVERT: D 446 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7897 (tpp80) REVERT: E 92 TYR cc_start: 0.8547 (m-10) cc_final: 0.8297 (m-10) REVERT: E 181 LYS cc_start: 0.8145 (tttt) cc_final: 0.7868 (tmtt) REVERT: E 212 LEU cc_start: 0.8180 (mt) cc_final: 0.7916 (mm) REVERT: E 455 PHE cc_start: 0.7746 (t80) cc_final: 0.7349 (t80) outliers start: 18 outliers final: 10 residues processed: 347 average time/residue: 2.0933 time to fit residues: 838.6377 Evaluate side-chains 346 residues out of total 1770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 334 time to evaluate : 2.509 ------------------------------------------------------------------------------- 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 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 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 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 111 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 47 GLN E 26 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 = 0.3590 r_free = 0.3590 target = 0.153592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.134189 restraints weight = 63218.939| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.46 r_work: 0.3242 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17305 Z= 0.159 Angle : 0.603 14.406 23605 Z= 0.303 Chirality : 0.040 0.212 2695 Planarity : 0.005 0.071 2825 Dihedral : 9.222 77.773 3383 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.95 % Allowed : 12.23 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.19), residues: 1960 helix: 2.14 (0.17), residues: 845 sheet: -0.15 (0.23), residues: 425 loop : 0.10 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 133 HIS 0.002 0.001 HIS B 297 PHE 0.012 0.002 PHE A 470 TYR 0.012 0.002 TYR A 31 ARG 0.014 0.001 ARG D 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 15) link_NAG-ASN : angle 4.64486 ( 45) link_BETA1-4 : bond 0.00316 ( 10) link_BETA1-4 : angle 1.89749 ( 30) hydrogen bonds : bond 0.04437 ( 826) hydrogen bonds : angle 4.81769 ( 2733) SS BOND : bond 0.00691 ( 10) SS BOND : angle 1.30898 ( 20) covalent geometry : bond 0.00349 (17270) covalent geometry : angle 0.56403 (23510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25338.04 seconds wall clock time: 436 minutes 31.02 seconds (26191.02 seconds total)